Markers of acute myeloid leukemia stem cells

ABSTRACT

Markers of acute myeloid leukemia stem cells (AMLSC) are identified. The markers are differentially expressed in comparison with normal counterpart cells, and are useful as diagnostic and therapeutic targets.

CROSS REFERENCE

This application claims benefit and is a Continuation of applicationSer. No. 14/927,349 filed Oct. 29, 2015, which is a a Continuation ofapplication Ser. No. 14/164,009 filed Jan. 24, 2014, now U.S. Pat. No.9,193,955 issued Nov. 24, 2015, which is a a Continuation of applicationSer. No. 13/739,788 filed Jan. 11, 2013, now U.S. Pat. No. 8,709,429issued Apr. 29, 2014, which is a a Continuation of application Ser. No.12/836,152 filed Jul. 14, 2010, now U.S. Pat. No. 8,361,736 issued Jan.29, 2013, which is a Continuation in Part and claims the benefit of PCTApplication No. PCT/US2009/000224, filed Jan. 13, 2009, which claimsbenefit of U.S. Provisional Patent Application No. 61/011,324, filedJan. 15, 2008, which applications are incorporated herein by referencein their entirety.

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made with Government support under contract CA086017awarded by the National Institutes of Health. The Government has certainrights in the invention.

BACKGROUND OF THE INVENTION

Basic cancer research has focused on identifying the genetic changesthat lead to cancer. This has led to major advances in our understandingof the molecular and biochemical pathways that are involved intumorigenesis and malignant transformation. However, our understandingof the cellular biology has lagged. Although the effects of particularmutations on the proliferation and survival of model cells, such asfibroblasts or cell lines, can be predicted, the effects of suchmutations on the actual cells involved in specific cancers is largelyguesswork.

A tumor can be viewed as an aberrant organ initiated by a tumorigeniccancer cell that acquired the capacity for indefinite proliferationthrough accumulated mutations. In this view of a tumor as an abnormalorgan, the principles of normal stem cell biology can be applied tobetter understand how tumors develop. Many observations suggest thatanalogies between normal stem cells and tumorigenic cells areappropriate. Both normal stem cells and tumorigenic cells have extensiveproliferative potential and the ability to give rise to new (normal orabnormal) tissues. Both tumors and normal tissues are composed ofheterogeneous combinations of cells, with different phenotypiccharacteristics and different proliferative potentials.

Because most tumors have a clonal origin, the original tumorigeniccancer cell gives rise to phenotypically diverse progeny, includingcancer cells with indefinite proliferative potential, as well as cancercells with limited or no proliferative potential. This suggests thattumorigenic cancer cells undergo processes that are analogous to theself-renewal and differentiation of normal stem cells. Tumorigenic cellscan be thought of as cancer stem cells that undergo an aberrant andpoorly regulated process of organogenesis analogous to what normal stemcells do. Although some of the heterogeneity in tumors arises as aresult of continuing mutagenesis, it is likely that heterogeneity alsoarises through the aberrant differentiation of cancer cells.

It is well documented that many types of tumors contain cancer cellswith heterogeneous phenotypes, reflecting aspects of the differentiationthat normally occurs in the tissues from which the tumors arise. Thevariable expression of normal differentiation markers by cancer cells ina tumor suggests that some of the heterogeneity in tumors arises as aresult of the anomalous differentiation of tumor cells. Examples of thisinclude the variable expression of myeloid markers in chronic myeloidleukaemia, the variable expression of neuronal markers within peripheralneurectodermal tumors, and the variable expression of milk proteins orthe estrogen receptor within breast cancer.

It was first extensively documented for leukemia and multiple myelomathat only a small subset of cancer cells is capable of extensiveproliferation. Because the differences in clonogenicity among theleukemia cells mirrored the differences in clonogenicity among normalhematopoietic cells, the clonogenic leukemic cells were described asleukemic stem cells. It has also been shown for solid cancers that thecells are phenotypically heterogeneous and that only a small proportionof cells are clonogenic in culture and in vivo. Just as in the contextof leukemic stem cells, these observations led to the hypothesis thatonly a few cancer cells are actually tumorigenic and that thesetumorigenic cells act as cancer stem cells.

In support of this hypothesis, recent studies have shown that, similarto leukemia and other hematologic malignancies, tumorigenic andnon-tumorigenic populations of breast cancer cells can be isolated basedon their expression of cell surface markers. In many cases of breastcancer, only a small subpopulation of cells had the ability to form newtumors. This work strongly supports the existence of CSC in breastcancer. Further evidence for the existence of cancer stem cellsoccurring in solid tumors has been found in central nervous system (CNS)malignancies. Using culture techniques similar to those used to culturenormal neuronal stem cells it has been shown that neuronal CNSmalignancies contain a small population of cancer cells that areclonogenic in vitro and initiate tumors in vivo, while the remainingcells in the tumor do not have these properties.

Stem cells are defined as cells that have the ability to perpetuatethemselves through self-renewal and to generate mature cells of aparticular tissue through differentiation. In most tissues, stem cellsare rare. As a result, stem cells must be identified prospectively andpurified carefully in order to study their properties. Perhaps the mostimportant and useful property of stem cells is that of self-renewal.Through this property, striking parallels can be found between stemcells and cancer cells: tumors may often originate from thetransformation of normal stem cells, similar signaling pathways mayregulate self-renewal in stem cells and cancer cells, and cancers maycomprise rare cells with indefinite potential for self-renewal thatdrive tumorigenesis.

The presence of cancer stem cells has profound implications for cancertherapy. At present, all of the phenotypically diverse cancer cells in atumor are treated as though they have unlimited proliferative potentialand can acquire the ability to metastasize. For many years, however, ithas been recognized that small numbers of disseminated cancer cells canbe detected at sites distant from primary tumors in patients that nevermanifest metastatic disease. One possibility is that immune surveillanceis highly effective at killing disseminated cancer cells before they canform a detectable tumor. Another possibility is that most cancer cellslack the ability to form a new tumor such, that only the disseminationof rare cancer stem cells can lead to metastatic disease. If so, thegoal of therapy must be to identify and kill this cancer stem cellpopulation.

The prospective identification and isolation of cancer stem cells willallow more efficient identification of diagnostic markers andtherapeutic targets expressed by the stem cells. Existing therapies havebeen developed largely against the bulk population of tumor cells,because the therapies are identified by their ability to shrink thetumor mass. However, because most cells within a cancer have limitedproliferative potential, an ability to shrink a tumor mainly reflects anability to kill these cells. Therapies that are more specificallydirected against cancer stem cells may result in more durable responsesand cures of metastatic tumors.

Hematopoiesis proceeds through an organized developmental hierarchyinitiated by hematopoietic stem cells (HSC) that give rise toprogressively more committed progenitors and eventually terminallydifferentiated blood cells. Although the concept of the HSC was not new,it was not until 1988 that it was shown that this population could beprospectively isolated from mouse bone marrow on the basis ofcell-surface markers using fluorescence-activated cell sorting (FACS).Since that time, the surface immunophenotype of the mouse HSC has becomeincreasingly refined, such that functional HSC can be isolated withexquisite sensitivity, resulting in a purity of 1 in 1.3 cells. Whileour ability to prospectively isolate mouse HSC has improved dramaticallyover the past 20 years, our understanding of the earliest events in thehuman hematopoietic system lags far behind.

Cancer stem cells are discussed in, for example, Pardal et al. (2003)Nat Rev Cancer 3, 895-902; Reya et al. (2001) Nature 414, 105-11; Bonnet& Dick (1997) Nat Med 3, 730-7; Al-Hajj et al. (2003) Proc Natl Acad SciUSA 100, 3983-8; Dontu et al. (2004) Breast Cancer Res 6, R605-15; Singhet al. (2004) Nature 432, 396-401.

The identification of a hierarchy of multipotent hematopoieticprogenitors in human cord blood, including multipotent progenitor cells,may be found in Majeti et al. (2007) Cell Stem Celli (6):635-45, hereinspecifically incorporated by reference, particularly with respect to theteaching of markers identifying the multipotent progentors.

SUMMARY OF THE INVENTION

Markers of acute myeloid leukemia stem cells (AMLSC) are providedherein. The markers are polynucleotides or polypeptides that aredifferentially expressed on AMLSC as compared to normal counterpartcells. Uses of the markers include use as targets for therapeuticantibodies or ligands; as targets for drug development, and foridentification or selection of AMLSC cell populations.

The AMLSC markers are useful as targets of therapeutic monoclonalantibodies for treatment of patients with de novo, relapsed, orrefractory acute myeloid leukemia. Such monoclonal antibodies are alsouseful in the treatment of pre-leukemic conditions, such asmyelodysplastic syndromes (MDS) and myeloproliferative disorders (MPDs)including: chronic myelogenous leukemia, polycythemia vera, essentialthrombocytosis, agnogenic myelofibrosis and myeloid metaplasia, andothers. Antibodies include free antibodies and antigen binding fragmentsderived therefrom, and conjugates, e.g. pegylated antibodies, drug,radioisotope, or toxin conjugates, and the like.

In some embodiments, combinations of monoclonal antibodies are used inthe treatment of human AML or pre-leukemic conditions. In oneembodiment, a monoclonal antibody directed against CD47, for example anantibody that blocks the interaction of CD47 with SIRPα, is combinedwith monoclonal antibodies directed against one or more additional AMLSCmarkers, e.g. CD96, CD97, CD99, CD180, PTHR2, HAVCR2 (also referred toas TIM3), and the like, which compositions can be synergistic inenhancing phagocytosis and elimination of AML LSC as compared to the useof single antibodies.

The AMLSC markers are useful as targets of monoclonal antibodies for usein ex vivo purging of autologous stem cell products (mobilizedperipheral blood or bone marrow) for use in autologous transplantationfor patients with acute myeloid leukemia or the pre-leukemic conditionsoutlined above. Combinations of monoclonal antibodies directed againstAML LSC-specific cell surface molecules, as described above, can besynergistic in eliminating LSC.

The AMLSC markers are useful in clinical diagnostic applicationsincluding, without limitation, primary diagnosis of AML or pre-leukemicconditions from blood and/or bone marrow specimens, evaluation ofleukemic involvement of the cerebrospinal and other body fluids,monitoring of interval disease progression, and monitoring of minimalresidual disease status.

As an alternative to monoclonal antibodies, the ligands of AMLSCmarkers, either as single agents or in combination, may be used totarget them in AML or the pre-leukemic conditions outlined above. Theligands can be free or conjugated, for direct administration to patientsor for ex vivo purging of autologous stem cell products. Some specificmolecules and their ligands include, without limitation, CD155-Fc fusionprotein that binds CD96; TIP39 that binds PTHR2; Galectin-9 that bindsHAVCR2.

The AMLSC cells can be prospectively isolated or identified from primarytumor samples, and possess the unique properties of cancer stem cells infunctional assays for cancer stem cell self-renewal and differentiation.

In some embodiments of the invention, methods are provided fordetection, classification or clinical staging of acute myeloid leukemiasaccording to the stem cells that are present in the leukemia, wheregreater numbers of stem cells are indicative of a more aggressive cancerphenotype. Staging is useful for prognosis and treatment. In someembodiments, a tumor sample is analyzed by histochemistry, includingimmunohistochemistry, in situ hybridization, and the like, for thepresence of CD34⁺CD38⁻ cells that express one or more AMLSC markersprovided herein. The presence of such cells indicates the presence ofAMLSC.

In another embodiment of the invention, methods for the isolation ofAMLSC are provided, comprising contacted a candidate cell populationwith a binding reagent specific for one or more of the AMLSC markersprovided herein, and selecting for cells that have bound to thereagent(s). The cells may further be selected as being CD34⁺CD38⁻. Thecells are useful for experimental evaluation, and as a source of lineageand cell specific products, including mRNA species useful in identifyinggenes specifically expressed in these cells, and as targets for thediscovery of factors or molecules that can affect them. AMLSC may beused, for example, in a method of screening a compound for an effect onthe cells. This involves combining the compound with the cell populationof the invention, and then determining any modulatory effect resultingfrom the compound. This may include examination of the cells forviability, toxicity, metabolic change, or an effect on cell function.The phenotype of AMLSC described herein provides a means of predictingdisease progression, relapse, and development of drug resistance.

BRIEF DESCRIPTION OF THE DRAWINGS

The invention is best understood from the following detailed descriptionwhen read in conjunction with the accompanying drawings. It isemphasized that, according to common practice, the various features ofthe drawings are not to-scale. On the contrary, the dimensions of thevarious features are arbitrarily expanded or reduced for clarity.Included in the drawings are the following figures.

FIG. 1A-1B: Differential Gene Expression Between AML LSC and Normal BoneMarrow HSC and MPP (FIG. 1A) Heat maps demonstrating genes found to bedifferentially expressed at least 2 fold between bone marrow HSC (n=4)and AML LSC (n=9) or bone marrow MPP (n=4) and AML LSC (n=9). Expressionrelative to the median is indicated for genes with p<0.05 and a FDR of5%. (FIG. 1B) Selected list of transmembrane proteins found to be atleast 2-fold more highly expressed in AML LSC than HSC of MPP. NS: notsignificant.

FIG. 2A-2B: CD47 is more highly expressed on AML LSC. Mobilizedperipheral blood (MPB) HSC and AML LSC were examined for CD47 expressionby flow cytometry. (FIG. 2A) Representative flow cytometry plotsindicating expression of CD47 relative to an isotype control. (FIG. 2B)Summary of CD47 expression on all samples assayed, with the indicatedmeans.

FIG. 3A-3C: Anti-CD47 Antibody Stimulates In Vitro MacrophagePhagocytosis of Primary Human AML LSC. AML LSC were purified by FACSfrom two primary human AML samples, labeled with the fluorescent dyeCFSE, and incubated with mouse bone marrow-derived macrophages either inthe presence of an isotype control (FIG. 3A) or anti-CD47 antibody (FIG.3B). These cells were assessed by immunofluorescence microscopy for thepresence of fluorescently labeled LSC within the macrophages. (FIG. 3C)The phagocytic index was determined for each condition by calculatingthe number of ingested cells per 100 macrophages.

FIG. 4A-4B: Anti-CD47 antibody stimulates in vitro macrophagephagocytosis of primary human AML LSC. AML LSC were purified by FACSfrom two primary human AML samples and labeled with the fluorescent dyeCFSE. These cells were incubated with mouse bone marrow-derivedmacrophages, either in the presence of an isotype matched control (left)or anti-CD47 antibody (right). The macrophages were harvested, stainedwith a fluorescently labeled anti-mouse macrophage antibody, andanalyzed by flow cytometry. mMac+CFSE+double-positive events identifymacrophages that have phagocytosed CFSE-labeled LSC. (FIG. 4A, 4B) twoindependent primary AML LSC samples.

FIG. 5: Anti-CD47 antibody inhibits in vivo engraftment of primary humanAML. Two primary human AML samples were untreated (control, n=3) orcoated with anti-human CD47 antibody (anti-CD47, n=6) prior totransplantation into newborn NOG mice. 13 weeks later, mice weresacrificed and the bone marrow was analyzed for the presence of humanCD45+CD33+myeloid leukemia cells by flow cytometry.

FIG. 6A-6B: CD99 Expression on AML LSC Compared to Normal HSC. CD99expression was examined on several samples of normal human bone marrowHSC (n=3) and de novo human AML LSC (n=7). Representative histograms ofCD99 expression on HSC and LSC (FIG. 6A) and summary of normalized meanfluorescence intensity (MFI) of all specimens (FIG. 6B) are shown. MeanCD99 expression was increased 5.6 fold in AML LSC compared to HSC(p=0.05).

FIG. 7A-7B: CD97 Expression on AML LSC Compared to Normal HSC. CD97expression was examined on several samples of normal human bone marrowHSC (n=3) and de novo human AML LSC (n=7). Representative histograms ofCD97 expression on HSC and LSC (FIG. 7A) and summary of normalized meanfluorescence intensity (MFI) of all specimens (FIG. 7B) are shown. MeanCD97 expression was increased 7.9 fold in AML LSC compared to HSC(p=0.03).

FIG. 8A-8B: CD180 Expression on AML LSC Compared to Normal HSC. CD180expression was examined on several samples of normal human bone marrowHSC (n=3) and de novo human AML LSC (n=7). Representative histograms ofCD180 expression on HSC and LSC (FIG. 8A) and summary of normalized meanfluorescence intensity (MFI) of all specimens (FIG. 8B) are shown. MeanCD180 expression was increased 60 fold in AML LSC compared to HSC(p=0.20).

FIG. 9A-9B: TIM3 Expression on AML LSC Compared to Normal HSC. TIM3expression was examined on several samples of normal human bone marrowHSC (n=3) and de novo human AML LSC (n=14). Representative histograms ofTIM3 expression on HSC and LSC (FIG. 9A) and summary of normalized meanfluorescence intensity (MFI) of all specimens (FIG. 9B) are shown. MeanTIM3 expression was increased 9 fold in AML LSC compared to HSC(p=0.01).

FIG. 10: PTH2R Expression in AML LSC Compared to Normal HSC. PTH2Rexpression was examined in several samples of normal human bone marrowHSC (n=3) and de novo human AML LSC (n=9). Expression was determined byqRT-PCR and is expressed relative to beta-actin as a control. Mean PTH2Rexpression was increased 21 fold in AML LSC compared to HSC (p<0.001).

FIG. 11A-11G: TIM-3 is More Highly Expressed on Functional AML LSC Thanon Functional NBM HSC. (FIG. 11A) Representative flow cytometryhistograms indicating TIM-3 expression on NBM HSC (Lin-CD34+CD38-CD90+)and AML LSC (Lin-CD34+CD38-CD90). (FIG. 11B) TIM-3 protein expressionwas assessed by flow cytometry for multiple specimens of NBM HSC,primary AML LSC, and bulk AML. Mean fluorescence intensity wasnormalized for cell size and against lineage-positive cells forcomparison between measurements conducted on different days. (FIG. 11C)The percentage of cells positive for TIM-3 expression by flow cytometrywithin the Lin-CD34+CD38− compartment of AML and normal bone marrowsamples was determined by comparison to isotype control. (FIG. 11D)TIM-3+ and TIM-3− fractions of the Lin-CD34+CD38− compartment fromnormal human bone marrow sample NBM05 were purified by two rounds offluorescence-activated cell sorting (FACS). Top panels demonstrateexpression of the indicated surface markers prior to sorting, while thebottom panels indicate results post-sorting. (FIG. 11E) These cells weretransplanted into NSG pups and, twelve weeks later, bone marrow wasanalyzed by flow cytometry for the presence of human CD45+leukocyteengraftment (left) whose lineage was further defined by expression ofCD19 on lymphoid cells and CD33 on myeloid cells (right). (FIG. 11F)TIM-3+ and TIM-3− fractions of the Lin-CD34+compartment from AML sampleSU018 were double-sorted by FACS. (FIG. 11G) These cells weretransplanted into NSG pups and 12 weeks later, human engraftment inmouse bone marrow was analyzed as above.

FIG. 12A-12F: Prospective Isolation of Residual Normal HSC From AMLPatient Samples. (FIG. 12A) TIM-3 expression was determined on theLin-CD34+CD38− fraction of AML sample SU031 by flow cytometry. TIM-3−and TIM-3+ cells were double-sorted to >99% purity by FACS. (FIG. 12B)These sorted cells were transplanted into NSG pups and, 12 weeks later,human engraftment in mouse bone marrow was analyzed. (FIG. 12C) RT-PCRfor the CBFB-MYH11 fusion transcript produced by inv(16) and humanβ-actin. (FIG. 12D) TIM-3 expression was determined on theLin-CD34+CD38− fraction of AML sample SU043 by flow cytometry. TIM-3−and TIM-3+ cells of were double-sorted to >98% purity by FACS. (FIG.12E) These sorted cells were plated in duplicate into completemethylcellulose media and, fourteen days later, myeloid colony formationwas determined by microscopy. (FIG. 12F) PCR of genomic DNA FLT3amplicon size identified wild-type FLT3 and FLT3-ITD. Note that in theleukemic cells, no wild-type FLT3 is detected indicating homozygousFLT3-ITD.

FIG. 13A-13D: Prospective Separation of Functional HSC and FunctionalAML LSC From a Single Patient Sample. (FIG. 13A) TIM-3 expression wasdetermined on the Lin-CD34+CD38− fraction of AML sample SU030 by flowcytometry. TIM-3+ and TIM-3− cells were double-sorted to >99% purity byFACS. (FIG. 13B) These sorted cells were plated in duplicate intocomplete methylcellulose media, and fourteen days later, myeloid colonyformation was determined by microscopy. A representative BFU-E is shown.(FIG. 13C) Lin-CD34+CD38-TIM-3+ and Lin-CD34+CD38-TIM-3− sorted cellswere transplanted into NSG pups and, 12 weeks later, human engraftmentin mouse bone marrow was analyzed. (FIG. 13D) PCR of genomic DNA forFLT3 amplicon size identified wild-type FLT3 and FLT3-ITD.

DETAILED DESCRIPTION OF THE EMBODIMENTS

The present invention identifies polynucleotides, as well aspolypeptides encoded thereby, that are differentially expressed in acutemyeloid leukemia stem cells (AMLSC). Methods are provided in which thesepolynucleotides and polypeptides, which may be collectively referred toas AMLSC markers, are used for detecting, assessing, and reducing thegrowth of cancer cells. Methods may use one or a combination of markers,where a combination may include 2, 3 or more markers, and in someembodiments will include CD47 in combination with 1, 2 or more markers.Other embodiments include TIM3 in combination with 1, 2 or more markers,including a combination of TIM3 and CD47, for example where antibodiesthat specifically bind to each of TIM3 and CD47 are used in theidentification, characterization and/or elimination of AMLSC. Theinvention finds use in the prevention, treatment, detection or researchof leukemic and pre-leukemic conditions.

The markers of the invention in some embodiments are expressed on theAMLSC cell surface. In some embodiments, the markers are expressed as alevel at least 2× the expression level of a counterpart non-transformedcell, e.g. a human hematopoietic stem cell, and/or a human hematopoieticmultipotent progenitor cell, where expression may be determined as thelevel of transcription, mRNA accumulation, and/or protein accumulation.In other embodiments the markers are expressed as a level at least 3×,at least 4×, at least 5×, at least 10×, at least 20× or greater, thanthe expression level of a counterpart non-transformed cell.

The present invention provides methods of using the markers describedherein in diagnosis of cancer, classification and treatment of leukemicand pre-leukemic conditions according to expression profiles. Themethods are useful for detecting AMLSC, facilitating diagnosis of AMLand the severity of the cancer (e.g., tumor grade, tumor burden, and thelike) in a subject, facilitating a determination of the prognosis of asubject, and assessing the responsiveness of the subject to therapy. Thedetection methods of the invention can be conducted in vitro or in vivo,on isolated cells, or in whole tissues or a bodily fluid, e.g., blood,lymph node biopsy samples, and the like.

As used herein, the terms “a gene that is differentially expressed in acancer stem cell,” and “a polynucleotide that is differentiallyexpressed in a cancer stem cell”, are used interchangeably herein, andgenerally refer to a polynucleotide that represents or corresponds to agene that is differentially expressed in a cancer stem cell whencompared with a cell of the same cell type that is not cancerous, e.g.,mRNA is found at levels at least about 25%, at least about 50% to about75%, at least about 90%, at least about 1.5-fold, at least about 2-fold,at least about 3-fold, at least about 5-fold, at least about 10-fold, orat least about 50-fold or more, different (e.g., higher or lower). Thecomparison can be made between AMLSC and the normal counterpart cells ahuman hematopoietic stem cell (HSC), which include without limitationcells having the phenotype Lin⁻CD34⁺CD38⁻CD90⁺; or the phenotypeLin⁻CD34⁺CD38⁻CD90⁺CD45RA⁻ and a human hematopoietic multipotentprogenitor cell (MPP), which include without limitation cells having thephenotype Lin⁻CD34⁺CD38⁻CD90⁻; or the phenotypeLin⁻CD34⁺CD38⁻CD9O⁻CD45RA⁻. The term “a polypeptide marker for a cancerstem cell” refers to a polypeptide encoded by a polynucleotide that isdifferentially expressed in a cancer stem cell.

In some embodiments of the invention, the markers are demonstrated byflow cytometry to be present on a majority of AMLSC, when compared tohuman HSC or MPP, as defined above. Such markers include, withoutlimitation, CD47, CD96, CD97, TIM3 and CD99.

In other embodiments of the invention, the markers are absent on humanHSC or human MPP, but are highly expressed on AMLSC. Such markersinclude, without limitation, those set forth in Table 1.

In other embodiments, the markers are differentially expressed on AMLSC,as compared to human HSC or MPP. Such markers include, withoutlimitation, those set forth in Table 1.

A polynucleotide or sequence that corresponds to, or represents a genemeans that at least a portion of a sequence of the polynucleotide ispresent in the gene or in the nucleic acid gene product (e.g., mRNA orcDNA). A subject nucleic acid may also be “identified” by apolynucleotide if the polynucleotide corresponds to or represents thegene. Genes identified by a polynucleotide may have all or a portion ofthe identifying sequence wholly present within an exon of a genomicsequence of the gene, or different portions of the sequence of thepolynucleotide may be present in different exons (e.g., such that thecontiguous polynucleotide sequence is present in an mRNA, either pre- orpost-splicing, that is an expression product of the gene). An“identifying sequence” is a minimal fragment of a sequence of contiguousnucleotides that uniquely identifies or defines a polynucleotidesequence or its complement.

The polynucleotide may represent or correspond to a gene that ismodified in a cancer stem cell (CSC) relative to a normal cell. The genein the CSC may contain a deletion, insertion, substitution, ortranslocation relative to the polynucleotide and may have alteredregulatory sequences, or may encode a splice variant gene product, forexample. The gene in the CSC may be modified by insertion of anendogenous retrovirus, a transposable element, or other naturallyoccurring or non-naturally occurring nucleic acid.

Sequences of interest include those set forth in Table 1, which aredifferentially expressed in AMLSC relative to normal counterpart cells.

Methods are also provided for optimizing therapy, by firstclassification, and based on that information, selecting the appropriatetherapy, dose, treatment modality, etc. which optimizes the differentialbetween delivery of an anti-proliferative treatment to the undesirabletarget cells, while minimizing undesirable toxicity. The treatment isoptimized by selection for a treatment that minimizes undesirabletoxicity, while providing for effective anti-proliferative activity.

The invention finds use in the prevention, treatment, detection orresearch of acute myeloid leukemias. Acute leukemias are rapidlyprogressing leukemia characterized by replacement of normal bone marrowby blast cells of a clone arising from malignant transformation of ahematopoietic stem cell. The acute leukemias include acute lymphoblasticleukemia (ALL) and acute myelogenous leukemia (AML). ALL often involvesthe CNS, whereas acute monoblastic leukemia involves the gums, and AMLinvolves localized collections in any site (granulocytic sarcomas orchloromas). AML is the most common acute leukemia affecting adults, andits incidence increases with age. While AML is a relatively rare diseaseoverall, accounting for approximately 1.2% of cancer deaths in theUnited States, its incidence is expected to increase as the populationages.

The presenting symptoms are usually nonspecific (e.g., fatigue, fever,malaise, weight loss) and reflect the failure of normal hematopoiesis.Anemia and thrombocytopenia are very common (75 to 90%). The WBC countmay be decreased, normal, or increased. Blast cells are usually found inthe blood smear unless the WBC count is markedly decreased. The blastsof ALL can be distinguished from those of AML by histochemical studies,cytogenetics, immunophenotyping, and molecular biology studies. Inaddition to smears with the usual stains, terminal transferase,myeloperoxidase, Sudan black B, and specific and nonspecific esterase.

“Diagnosis” as used herein generally includes determination of asubject's susceptibility to a disease or disorder, determination as towhether a subject is presently affected by a disease or disorder,prognosis of a subject affected by a disease or disorder (e.g.,identification of cancerous states, stages of cancer, or responsivenessof cancer to therapy), and use of therametrics (e.g., monitoring asubject's condition to provide information as to the effect or efficacyof therapy).

The term “biological sample” encompasses a variety of sample typesobtained from an organism and can be used in a diagnostic or monitoringassay. The term encompasses blood and other liquid samples of biologicalorigin, solid tissue samples, such as a biopsy specimen or tissuecultures or cells derived therefrom and the progeny thereof. The termencompasses samples that have been manipulated in any way after theirprocurement, such as by treatment with reagents, solubilization, orenrichment for certain components. The term encompasses a clinicalsample, and also includes cells in cell culture, cell supernatants, celllysates, serum, plasma, biological fluids, and tissue samples.

The terms “treatment”, “treating”, “treat” and the like are used hereinto generally refer to obtaining a desired pharmacologic and/orphysiologic effect. The effect may be prophylactic in terms ofcompletely or partially preventing a disease or symptom thereof and/ormay be therapeutic in terms of a partial or complete stabilization orcure for a disease and/or adverse effect attributable to the disease.“Treatment” as used herein covers any treatment of a disease in amammal, particularly a human, and includes: (a) preventing the diseaseor symptom from occurring in a subject which may be predisposed to thedisease or symptom but has not yet been diagnosed as having it; (b)inhibiting the disease symptom, i.e., arresting its development; or (c)relieving the disease symptom, i.e., causing regression of the diseaseor symptom.

The terms “individual,” “subject,” “host,” and “patient,” usedinterchangeably herein and refer to any mammalian subject for whomdiagnosis, treatment, or therapy is desired, particularly humans.

A “host cell”, as used herein, refers to a microorganism or a eukaryoticcell or cell line cultured as a unicellular entity which can be, or hasbeen, used as a recipient for a recombinant vector or other transferpolynucleotides, and include the progeny of the original cell which hasbeen transfected. It is understood that the progeny of a single cell maynot necessarily be completely identical in morphology or in genomic ortotal DNA complement as the original parent, due to natural, accidental,or deliberate mutation.

The terms “cancer”, “neoplasm”, “tumor”, and “carcinoma”, are usedinterchangeably herein to refer to cells which exhibit relativelyautonomous growth, so that they exhibit an aberrant growth phenotypecharacterized by a significant loss of control of cell proliferation. Ingeneral, cells of interest for detection or treatment in the presentapplication include precancerous (e.g., benign), malignant,pre-metastatic, metastatic, and non-metastatic cells. Detection ofcancerous cells is of particular interest. The term “normal” as used inthe context of “normal cell,” is meant to refer to a cell of anuntransformed phenotype or exhibiting a morphology of a non-transformedcell of the tissue type being examined. “Cancerous phenotype” generallyrefers to any of a variety of biological phenomena that arecharacteristic of a cancerous cell, which phenomena can vary with thetype of cancer. The cancerous phenotype is generally identified byabnormalities in, for example, cell growth or proliferation (e.g.,uncontrolled growth or proliferation), regulation of the cell cycle,cell mobility, cell-cell interaction, or metastasis, etc.

“Therapeutic target” refers to a gene or gene product that, uponmodulation of its activity (e.g., by modulation of expression,biological activity, and the like), can provide for modulation of thecancerous phenotype. As used throughout, “modulation” is meant to referto an increase or a decrease in the indicated phenomenon (e.g.,modulation of a biological activity refers to an increase in abiological activity or a decrease in a biological activity).

Acute Myeloid Leukemia

Acute Myelocytic Leukemia (AML, Acute Myelogenous Leukemia; AcuteMyeloid Leukemia). In AML, malignant transformation and uncontrolledproliferation of an abnormally differentiated, long-lived myeloidprogenitor cell results in high circulating numbers of immature bloodforms and replacement of normal marrow by malignant cells. Symptomsinclude fatigue, pallor, easy bruising and bleeding, fever, andinfection; symptoms of leukemic infiltration are present in only about5% of patients (often as skin manifestations). Examination of peripheralblood smear and bone marrow is diagnostic. Treatment includes inductionchemotherapy to achieve remission and post-remission chemotherapy (withor without stem cell transplantation) to avoid relapse.

AML has a number of subtypes that are distinguished from each other bymorphology, immunophenotype, and cytochemistry. Five classes aredescribed, based on predominant cell type, including myeloid,myeloid-monocytic, monocytic, erythroid, and megakaryocytic. Acutepromyelocytic leukemia is a particularly important subtype, representing10 to 15% of all cases of AML, striking a younger age group (median age31 yr) and particular ethnicity (Hispanics), in which the patientcommonly presents with a coagulation disorder.

Remission induction rates range from 50 to 85%. Long-term disease-freesurvival reportedly occurs in 20 to 40% of patients and increases to 40to 50% in younger patients treated with stem cell transplantation.

Prognostic factors help determine treatment protocol and intensity;patients with strongly negative prognostic features are usually givenmore intense forms of therapy, because the potential benefits arethought to justify the increased treatment toxicity. The most importantprognostic factor is the leukemia cell karyotype; favorable karyotypesinclude t(15;17), t(8;21), and inv16 (p13;q22). Negative factors includeincreasing age, a preceding myelodysplastic phase, secondary leukemia,high WBC count, and absence of Auer rods. The FAB or WHO classificationalone does not predict response.

Initial therapy attempts to induce remission and differs most from ALLin that AML responds to fewer drugs. The basic induction regimenincludes cytarabine by continuous IV infusion or high doses for 5 to 7days; daunorubicin or idarubicin is given IV for 3 days during thistime. Some regimens include 6-thioguanine, etoposide, vincristine, andprednisone, but their contribution is unclear. Treatment usually resultsin significant myelosuppression, with infection or bleeding; there issignificant latency before marrow recovery. During this time, meticulouspreventive and supportive care is vital.

Polypeptide and Polynucleotide Sequences and Antibodies

The invention provides polynucleotides and polypeptides that representgenes that are differentially expressed in human AMLSC. Thesepolynucleotides, polypeptides and fragments thereof have uses thatinclude, but are not limited to, diagnostic probes and primers asstarting materials for probes and primers, as immunogens for antibodiesuseful in cancer diagnosis and therapy, and the like as discussedherein.

Nucleic acid compositions include fragments and primers, and are atleast about 15 bp in length, at least about 30 bp in length, at leastabout 50 bp in length, at least about 100 bp, at least about 200 bp inlength, at least about 300 bp in length, at least about 500 bp inlength, at least about 800 bp in length, at least about 1 kb in length,at least about 2.0 kb in length, at least about 3.0 kb in length, atleast about 5 kb in length, at least about 10 kb in length, at leastabout 50 kb in length and are usually less than about 200 kb in length.In some embodiments, a fragment of a polynucleotide is the codingsequence of a polynucleotide. Also included are variants or degeneratevariants of a sequence provided herein. In general, variants of apolynucleotide provided herein have a fragment of sequence identity thatis greater than at least about 65%, greater than at least about 70%,greater than at least about 75%, greater than at least about 80%,greater than at least about 85%, or greater than at least about 90%,95%, 96%, 97%, 98%, 99% /0 or more (i.e. 100%) as compared to anidentically sized fragment of a provided sequence. as determined by theSmith-Waterman homology search algorithm as implemented in MPSRCHprogram (Oxford Molecular). Nucleic acids having sequence similarity canbe detected by hybridization under low stringency conditions, forexample, at 50° C. and 10× SSC (0.9 M saline/0.09 M sodium citrate) andremain bound when subjected to washing at 55° C. in 1× SSC. Sequenceidentity can be determined by hybridization under high stringencyconditions, for example, at 50° C. or higher and 0.1× SSC (9 mMsaline/0.9 mM sodium citrate). Hybridization methods and conditions arewell known in the art, see, e.g., U.S. Pat. No. 5,707,829. Nucleic acidsthat are substantially identical to the provided polynucleotidesequences, e.g. allelic variants, genetically altered versions of thegene, etc., bind to the provided polynucleotide sequences understringent hybridization conditions.

Probes specific to the polynucleotides described herein can be generatedusing the polynucleotide sequences disclosed herein. The probes areusually a fragment of a polynucleotide sequences provided herein. Theprobes can be synthesized chemically or can be generated from longerpolynucleotides using restriction enzymes. The probes can be labeled,for example, with a radioactive, biotinylated, or fluorescent tag.Preferably, probes are designed based upon an identifying sequence ofany one of the polynucleotide sequences provided herein.

The nucleic acid compositions described herein can be used to, forexample, produce polypeptides, as probes for the detection of mRNA inbiological samples (e.g., extracts of human cells) or cDNA produced fromsuch samples, to generate additional copies of the polynucleotides, togenerate ribozymes or antisense oligonucleotides, and as single strandedDNA probes or as triple-strand forming oligonucleotides.

The probes described herein can be used to, for example, determine thepresence or absence of any one of the polynucleotide provided herein orvariants thereof in a sample. These and other uses are described in moredetail below. In one embodiment, real time PCR analysis is used toanalyze gene expression.

The polypeptides contemplated by the invention include those encoded bythe disclosed polynucleotides and the genes to which thesepolynucleotides correspond, as well as nucleic acids that, by virtue ofthe degeneracy of the genetic code, are not identical in sequence to thedisclosed polynucleotides. Further polypeptides contemplated by theinvention include polypeptides that are encoded by polynucleotides thathybridize to polynucleotide of the sequence listing. Thus, the inventionincludes within its scope a polypeptide encoded by a polynucleotidehaving the sequence of any one of the polynucleotide sequences providedherein, or a variant thereof.

In general, the term “polypeptide” as used herein refers to both thefull length polypeptide encoded by the recited polynucleotide, thepolypeptide encoded by the gene represented by the recitedpolynucleotide, as well as portions or fragments thereof. “Polypeptides”also includes variants of the naturally occurring proteins, where suchvariants are homologous or substantially similar to the naturallyoccurring protein, and can be of an origin of the same or differentspecies as the naturally occurring protein. In general, variantpolypeptides have a sequence that has at least about 80%, usually atleast about 90%, and more usually at least about 98% sequence identitywith a differentially expressed polypeptide described herein. Thevariant polypeptides can be naturally or non-naturally glycosylated,i.e., the polypeptide has a glycosylation pattern that differs from theglycosylation pattern found in the corresponding naturally occurringprotein.

Fragments of the polypeptides disclosed herein, particularlybiologically active fragments and/or fragments corresponding tofunctional domains, are of interest. Fragments of interest willtypically be at least about 10 aa to at least about 15 aa in length,usually at least about 50 aa in length, and can be as long as 300 aa inlength or longer, but will usually not exceed about 1000 aa in length,where the fragment will have a stretch of amino acids that is identicalto a polypeptide encoded by a polynucleotide having a sequence of anyone of the polynucleotide sequences provided herein, or a homologthereof. A fragment “at least 20 aa in length,” for example, is intendedto include 20 or more contiguous amino acids from, for example, thepolypeptide encoded by a cDNA, in a cDNA clone contained in a depositedlibrary or the complementary stand thereof. In this context “about”includes the particularly recited value or a value larger or smaller byseveral (5, 4, 3, 2, or 1) amino acids. The protein variants describedherein are encoded by polynucleotides that are within the scope of theinvention. The genetic code can be used to select the appropriate codonsto construct the corresponding variants. The polynucleotides may be usedto produce polypeptides, and these polypeptides may be used to produceantibodies by known methods described above and below.

A polypeptide of this invention can be recovered and purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxylapatitechromatography and lectin chromatography. Most preferably, highperformance liquid chromatography (“HPLC”) is employed for purification.

Polypeptides can also be recovered from: products purified from naturalsources, including bodily fluids, tissues and cells, whether directlyisolated or cultured; products of chemical synthetic procedures; andproducts produced by recombinant techniques from a prokaryotic oreukaryotic host, including, for example, bacterial, yeast higher plant,insect, and mammalian cells.

Gene products, including polypeptides, mRNA (particularly mRNAs havingdistinct secondary and/or tertiary structures), cDNA, or complete gene,can be prepared and used for raising antibodies for experimental,diagnostic, and therapeutic purposes. Antibodies may be used to identifyAMLSC cells or subtypes. The polynucleotide or related cDNA is expressedas described herein, and antibodies are prepared. These antibodies arespecific to an epitope on the polypeptide encoded by the polynucleotide,and can precipitate or bind to the corresponding native protein in acell or tissue preparation or in a cell-free extract of an in vitroexpression system.

The antibodies may be utilized for immunophenotyping of cells andbiological samples. The translation product of a differentiallyexpressed gene may be useful as a marker. Monoclonal antibodies directedagainst a specific epitope, or combination of epitopes, will allow forthe screening of cellular populations expressing the marker. Varioustechniques can be utilized using monoclonal antibodies to screen forcellular populations expressing the marker(s), and include magneticseparation using antibody-coated magnetic beads, “panning” with antibodyattached to a solid matrix (i.e., plate), and flow cytometry (See, e.g.,U.S. Pat. No. 5,985,660; and Morrison et al. Cell, 96:737-49 (1999)).These techniques allow for the screening of particular populations ofcells; in immunohistochemistry of biopsy samples; in detecting thepresence of markers shed by cancer cells into the blood and otherbiologic fluids, and the like.

In many embodiments, the levels of a subject gene or gene product aremeasured. By measured is meant qualitatively or quantitativelyestimating the level of the gene product in a first biological sampleeither directly (e.g. by determining or estimating absolute levels ofgene product) or relatively by comparing the levels to a second controlbiological sample. In many embodiments the second control biologicalsample is obtained from an individual not having cancer. As will beappreciated in the art, once a standard control level of gene expressionis known, it can be used repeatedly as a standard for comparison. Othercontrol samples include samples of cancerous tissue.

The methods can be used to detect and/or measure mRNA levels of a genethat is differentially expressed in a cancer cell. In some embodiments,the methods comprise: contacting a sample with a polynucleotide thatcorresponds to a differentially expressed gene described herein underconditions that allow hybridization; and detecting hybridization, ifany. Detection of differential hybridization, when compared to asuitable control, is an indication of the presence in the sample of apolynucleotide that is differentially expressed in a cancer cell.Appropriate controls include, for example, a sample that is known not tocontain a polynucleotide that is differentially expressed in a cancercell. Conditions that allow hybridization are known in the art, and havebeen described in more detail above.

Detection can also be accomplished by any known method, including, butnot limited to, in situ hybridization, PCR (polymerase chain reaction),RT-PCR (reverse transcription-PCR), and “Northern” or RNA blotting,arrays, microarrays, etc, or combinations of such techniques, using asuitably labeled polynucleotide. A variety of labels and labelingmethods for polynucleotides are known in the art and can be used in theassay methods of the invention. Specific hybridization can be determinedby comparison to appropriate controls.

Labeled nucleic acid probes may be used to detect expression of a genecorresponding to the provided polynucleotide, e.g. in a macroarrayformat, Northern blot, etc. The amount of hybridization can bequantitated to determine relative amounts of expression, for exampleunder a particular condition. Probes are used for in situ hybridizationto cells to detect expression. Probes can also be used in vivo fordiagnostic detection of hybridizing sequences. Probes may be labeledwith a radioactive isotope. Other types of detectable labels can be usedsuch as chromophores, fluorophores, and enzymes.

Polynucleotide arrays provide a high throughput technique that can assaya large number of polynucleotides or polypeptides in a sample. Thistechnology can be used as a tool to test for differential expression. Avariety of methods of producing arrays, as well as variations of thesemethods, are known in the art and contemplated for use in the invention.For example, arrays can be created by spotting polynucleotide probesonto a substrate (e.g., glass, nitrocellulose, etc.) in atwo-dimensional matrix or array having bound probes. The probes can bebound to the substrate by either covalent bonds or by non-specificinteractions, such as hydrophobic interactions.

Characterization of Acute Myeloid Leukemia Stem Cells

In acute myeloid leukemias, characterization of cancer stem cells allowsfor the development of new treatments that are specifically targetedagainst this critical population of cells, particularly their ability toself-renew, resulting in more effective therapies.

In human acute myeloid leukemias it is shown herein that there is asubpopulation of tumorigenic cancer cells with both self-renewal anddifferentiation capacity. These tumorigenic cells are responsible fortumor maintenance, and also give rise to large numbers of abnormallydifferentiating progeny that are not tumorigenic, thus meeting thecriteria of cancer stem cells. Tumorigenic potential is contained withina subpopulation of cancer cells differentially expressing the markers ofthe present invention.

In some embodiments of the invention, the number of AMLSC in a patientsample is determined relative to the total number of AML cancer cells,where a greater percentage of AMLSC is indicative of the potential forcontinued self-renewal of cells with the cancer phenotype. Thequantitation of AMLSC in a patient sample may be compared to a referencepopulation, e.g. a patient sample such as a blood sample, a remissionpatient sample, etc. In some embodiments, the quantitation of AMLSC isperformed during the course of treatment, where the number of AML cancercells and the percentage of such cells that are AMLSC are quantitatedbefore, during and as follow-up to a course of therapy. Desirably,therapy targeted to cancer stem cells results in a decrease in the totalnumber, and/or percentage of AMLSC in a patient sample.

In other embodiments of the invention, anti-cancer agents are targetedto AMLSC by specific binding to a marker or combination of markers ofthe present invention. In such embodiments, the anti-cancer agentsinclude antibodies and antigen-binding derivatives thereof specific fora marker or combination of markers of the present invention, which areoptionally conjugated to a cytotoxic moiety. Depletion of AMLSC isuseful in the treatment of AML. Depletion achieves a reduction incirculating AMLSC by up to about 30%, or up to about 40%, or up to about50%, or up to about 75% or more. Depletion can be achieved by using a anagent to deplete AMLSC either in vivo or ex vivo.

The AMLSC are identified by their phenotype with respect to particularmarkers, and/or by their functional phenotype. In some embodiments, theAMLSC are identified and/or isolated by binding to the cell withreagents specific for the markers of interest. The cells to be analyzedmay be viable cells, or may be fixed or embedded cells.

In some embodiments, the reagents specific for the markers of interestare antibodies, which may be directly or indirectly labeled. Suchantibodies will usually include antibodies specific for a marker orcombination of markers of the present invention.

Treatment of Cancer

The invention further provides methods for reducing growth of cancercells. The methods provide for decreasing the number of cancer cellsbearing a specific marker or combination of markers, as provided herein,decreasing expression of a gene that is differentially expressed in acancer cell, or decreasing the level of and/or decreasing an activity ofa cancer-associated polypeptide. In general, the methods comprisecontacting a cancer cell with a binding agent, e.g. an antibody orligand specific for a marker or combination of markers provided herein.

“Reducing growth of cancer cells” includes, but is not limited to,reducing proliferation of cancer cells, and reducing the incidence of anon-cancerous cell becoming a cancerous cell. Whether a reduction incancer cell growth has been achieved can be readily determined using anyknown assay, including, but not limited to, [³H]-thymidineincorporation; counting cell number over a period of time; detectingand/or measuring a marker associated with AML, etc.

The present invention provides methods for treating cancer, generallycomprising administering to an individual in need thereof a substancethat reduces cancer cell growth, in an amount sufficient to reducecancer cell growth and treat the cancer. Whether a substance, or aspecific amount of the substance, is effective in treating cancer can beassessed using any of a variety of known diagnostic assays for cancer,including, but not limited to biopsy, contrast radiographic studies, CATscan, and detection of a tumor marker associated with cancer in theblood of the individual. The substance can be administered systemicallyor locally, usually systemically.

A substance, e.g. a chemotherapeutic drug that reduces cancer cellgrowth, can be targeted to a cancer cell. Thus, in some embodiments, theinvention provides a method of delivering a drug to a cancer cell,comprising administering a drug-antibody complex to a subject, whereinthe antibody is specific for a cancer-associated polypeptide, and thedrug is one that reduces cancer cell growth, a variety of which areknown in the art. Targeting can be accomplished by coupling (e.g.,linking, directly or via a linker molecule, either covalently ornon-covalently, so as to form a drug-antibody complex) a drug to anantibody specific for a cancer-associated polypeptide. Methods ofcoupling a drug to an antibody are well known in the art and need not beelaborated upon herein.

Staging and Diagnosis

Acute myeloid leukemias are staged by analysis of the presence of cancerstem cells. Staging is useful for prognosis and treatment. In oneembodiment of the invention, a sample from an acute myeloid leukemiapatient is stained with reagents specific for a marker or combination ofmarkers of the present invention. The analysis of staining patternsprovides the relative distribution of AMLSC, which distribution predictsthe stage of leukemia. In some embodiments, the sample is analyzed byhistochemistry, including immunohistochemistry, in situ hybridization,and the like, for the presence of CD34⁺CD38⁻cells that express a markeror combination of markers of the present invention. The presence of suchcells indicates the presence of AMLSC.

In one embodiment, the patient sample is compared to a control, or astandard test value. In another embodiment, the patient sample iscompared to a pre-leukemia sample, or to one or more time points throughthe course of the disease.

Samples, including tissue sections, slides, etc. containing an acutemyeloid leukemia tissue, are stained with reagents specific for markersthat indicate the presence of cancer stem cells. Samples may be frozen,embedded, present in a tissue microarray, and the like. The reagents,e.g. antibodies, polynucleotide probes, etc. may be detectably labeled,or may be indirectly labeled in the staining procedure. The dataprovided herein demonstrate that the number and distribution ofprogenitor cells is diagnostic of the stage of the leukemia.

The information thus derived is useful in prognosis and diagnosis,including susceptibility to acceleration of disease, status of adiseased state and response to changes in the environment, such as thepassage of time, treatment with drugs or other modalities. The cells canalso be classified as to their ability to respond to therapeutic agentsand treatments, isolated for research purposes, screened for geneexpression, and the like. The clinical samples can be furthercharacterized by genetic analysis, proteomics, cell surface staining, orother means, in order to determine the presence of markers that areuseful in classification. For example, genetic abnormalities can becausative of disease susceptibility or drug responsiveness, or can belinked to such phenotypes.

Differential Cell Analysis

The presence of AMLSC in a patient sample can be indicative of the stageof the leukemia. In addition, detection of AMLSC can be used to monitorresponse to therapy and to aid in prognosis. The presence of AMLSC canbe determined by quantitating the cells having the phenotype of the stemcell. In addition to cell surface phenotyping, it may be useful toquantitate the cells in a sample that have a “stem cell” character,which may be determined by functional criteria, such as the ability toself-renew, to give rise to tumors in vivo, e.g. in a xenograft model,and the like.

Clinical samples for use in the methods of the invention may be obtainedfrom a variety of sources, particularly blood, although in someinstances samples such as bone marrow, lymph, cerebrospinal fluid,synovial fluid, and the like may be used. Such samples can be separatedby centrifugation, elutriation, density gradient separation, apheresis,affinity selection, panning, FACS, centrifugation with Hypaque, etc.prior to analysis, and usually a mononuclear fraction (PBMC) will beused. Once a sample is obtained, it can be used directly, frozen, ormaintained in appropriate culture medium for short periods of time.Various media can be employed to maintain cells. The samples may beobtained by any convenient procedure, such as the drawing of blood,venipuncture, biopsy, or the like. Usually a sample will comprise atleast about 10² cells, more usually at least about 10³ cells, andpreferable 10⁴, 10⁵ or more cells. Typically the samples will be fromhuman patients, although animal models may find use, e.g. equine,bovine, porcine, canine, feline, rodent, e.g. mice, rats, hamster,primate, etc.

An appropriate solution may be used for dispersion or suspension of thecell sample. Such solution will generally be a balanced salt solution,e.g. normal saline, PBS, Hank's balanced salt solution, etc.,conveniently supplemented with fetal calf serum or other naturallyoccurring factors, in conjunction with an acceptable buffer at lowconcentration, generally from 5-25 mM. Convenient buffers include HEPES,phosphate buffers, lactate buffers, etc.

Analysis of the cell staining will use conventional methods. Techniquesproviding accurate enumeration include fluorescence activated cellsorters, which can have varying degrees of sophistication, such asmultiple color channels, low angle and obtuse light scattering detectingchannels, impedance channels, etc. The cells may be selected againstdead cells by employing dyes associated with dead cells (e.g. propidiumiodide).

The affinity reagents may be specific receptors or ligands for the cellsurface molecules indicated above. In addition to antibody reagents,peptide-MHC antigen and T cell receptor pairs may be used; peptideligands and receptors; effector and receptor molecules, and the like.Antibodies and T cell receptors may be monoclonal or polyclonal, and maybe produced by transgenic animals, immunized animals, immortalized humanor animal B-cells, cells transfected with DNA vectors encoding theantibody or T cell receptor, etc. The details of the preparation ofantibodies and their suitability for use as specific binding members arewell-known to those skilled in the art.

Of particular interest is the use of antibodies as affinity reagents.Conveniently, these antibodies are conjugated with a label for use inseparation. Labels include magnetic beads, which allow for directseparation, biotin, which can be removed with avidin or streptavidinbound to a support, fluorochromes, which can be used with a fluorescenceactivated cell sorter, or the like, to allow for ease of separation ofthe particular cell type. Fluorochromes that find use includephycobiliproteins, e.g. phycoerythrin and allophycocyanins, fluoresceinand Texas red. Frequently each antibody is labeled with a differentfluorochrome, to permit independent sorting for each marker.

The antibodies are added to a suspension of cells, and incubated for aperiod of time sufficient to bind the available cell surface antigens.The incubation will usually be at least about 5 minutes and usually lessthan about 30 minutes. It is desirable to have a sufficientconcentration of antibodies in the reaction mixture, such that theefficiency of the separation is not limited by lack of antibody. Theappropriate concentration is determined by titration. The medium inwhich the cells are separated will be any medium that maintains theviability of the cells. A preferred medium is phosphate buffered salinecontaining from 0.1 to 0.5% BSA. Various media are commerciallyavailable and may be used according to the nature of the cells,including Dulbecco's Modified Eagle Medium (dMEM), Hank's Basic SaltSolution (HBSS), Dulbecco's phosphate buffered saline (dPBS), RPMI,Iscove's medium, PBS with 5 mM EDTA, etc., frequently supplemented withfetal calf serum, BSA, HSA, etc.

The labeled cells are then quantitated as to the expression of cellsurface markers as previously described.

The comparison of a differential progenitor analysis obtained from apatient sample, and a reference differential progenitor analysis isaccomplished by the use of suitable deduction protocols, Al systems,statistical comparisons, etc. A comparison with a reference differentialprogenitor analysis from normal cells, cells from similarly diseasedtissue, and the like, can provide an indication of the disease staging.A database of reference differential progenitor analyses can becompiled. An analysis of particular interest tracks a patient, e.g. inthe chronic and pre-leukemic stages of disease, such that accelerationof disease is observed at an early stage. The methods of the inventionprovide detection of acceleration prior to onset of clinical symptoms,and therefore allow early therapeutic intervention, e.g. initiation ofchemotherapy, increase of chemotherapy dose, changing selection ofchemotherapeutic drug, and the like.

AMLSC Compositions

AMLSC may be separated from a complex mixture of cells by techniquesthat enrich for cells that differentially express a marker orcombination of markers of the present invention. For isolation of cellsfrom tissue, an appropriate solution may be used for dispersion orsuspension. Such solution will generally be a balanced salt solution,e.g. normal saline, PBS, Hank's balanced salt solution, etc.,conveniently supplemented with fetal calf serum or other naturallyoccurring factors, in conjunction with an acceptable buffer at lowconcentration, generally from 5-25 mM. Convenient buffers include HEPES,phosphate buffers, lactate buffers, etc.

The separated cells may be collected in any appropriate medium thatmaintains the viability of the cells, usually having a cushion of serumat the bottom of the collection tube. Various media are commerciallyavailable and may be used according to the nature of the cells,including dMEM, HBSS, dPBS, RPMI, Iscove's medium, etc., frequentlysupplemented with fetal calf serum.

Compositions highly enriched for AMLSC are achieved in this manner. Thesubject population may be at or about 50% or more of the cellcomposition, and preferably be at or about 75% or more of the cellcomposition, and may be 90% or more. The desired cells are identified bytheir surface phenotype, by the ability to self-renew, ability to formtumors, etc. The enriched cell population may be used immediately, ormay be frozen at liquid nitrogen temperatures and stored for longperiods of time, being thawed and capable of being reused. The cells maybe stored in 10% DMSO, 90% FCS medium. The population of cells enrichedfor AMLSC may be used in a variety of screening assays and cultures, asdescribed below.

The enriched AMLSC population may be grown in vitro under variousculture conditions. Culture medium may be liquid or semi-solid, e.g.containing agar, methylcellulose, etc. The cell population may beconveniently suspended in an appropriate nutrient medium, such asIscove's modified DMEM or RPMI-1640, normally supplemented with fetalcalf serum (about 5-10%), L-glutamine, a thiol, particularly2-mercaptoethanol, and antibiotics, e.g. penicillin and streptomycin.

The culture may contain growth factors to which the cells areresponsive. Growth factors, as defined herein, are molecules capable ofpromoting survival, growth and/or differentiation of cells, either inculture or in the intact tissue, through specific effects on atransmembrane receptor. Growth factors include polypeptides andnon-polypeptide factors. A wide variety of growth factors may be used inculturing the cells, e.g. LIF, steel factor (c-kit ligand), EGF,insulin, IGF, Flk-2 ligand, IL-11, IL-3, GM-CSF, erythropoietin,thrombopoietin, etc

In addition to, or instead of growth factors, the subject cells may begrown in a co-culture with fibroblasts, stromal or other feeder layercells. Stromel cells suitable for use in the growth of hematopoieticcells are known in the art. These include bone marrow stroma as used in“Whitlock-Witte” (Whitlock et al. [1985] Annu Rev Immunol 3:213-235) or“Dexter” culture conditions (Dexter et al. [1977] J Exp Med145:1612-1616); and heterogeneous thymic stromal cells.

Screening Assays

AMLSC expressing a marker or combination of markers of the presentinvention are also useful for in vitro assays and screening to detectfactors and chemotherapeutic agents that are active on cancer stemcells. Of particular interest are screening assays for agents that areactive on human cells. A wide variety of assays may be used for thispurpose, including immunoassays for protein binding; determination ofcell growth, differentiation and functional activity; production offactors; and the like. In other embodiments, isolated polypeptidescorresponding to a marker or combination of markers of the presentinvention are useful in drug screening assays.

In screening assays for biologically active agents, anti-proliferativedrugs, etc. the marker or AMLSC composition is contacted with the agentof interest, and the effect of the agent assessed by monitoring outputparameters on cells, such as expression of markers, cell viability, andthe like; or binding efficacy or effect on enzymatic or receptoractivity for polypeptides. The cells may be freshly isolated, cultured,genetically altered, and the like. The cells may be environmentallyinduced variants of clonal cultures: e.g. split into independentcultures and grown under distinct conditions, for example with orwithout drugs; in the presence or absence of cytokines or combinationsthereof. The manner in which cells respond to an agent, particularly apharmacologic agent, including the timing of responses, is an importantreflection of the physiologic state of the cell.

Parameters are quantifiable components of cells, particularly componentsthat can be accurately measured, desirably in a high throughput system.A parameter can be any cell component or cell product including cellsurface determinant, receptor, protein or conformational orposttranslational modification thereof, lipid, carbohydrate, organic orinorganic molecule, nucleic acid, e.g. mRNA, DNA, etc. or a portionderived from such a cell component or combinations thereof. While mostparameters will provide a quantitative readout, in some instances asemi-quantitative or qualitative result will be acceptable. Readouts mayinclude a single determined value, or may include mean, median value orthe variance, etc. Characteristically a range of parameter readoutvalues will be obtained for each parameter from a multiplicity of thesame assays. Variability is expected and a range of values for each ofthe set of test parameters will be obtained using standard statisticalmethods with a common statistical method used to provide single values.

Agents of interest for screening include known and unknown compoundsthat encompass numerous chemical classes, primarily organic molecules,which may include organometallic molecules, inorganic molecules, geneticsequences, etc. An important aspect of the invention is to evaluatecandidate drugs, including toxicity testing; and the like.

In addition to complex biological agents candidate agents includeorganic molecules comprising functional groups necessary for structuralinteractions, particularly hydrogen bonding, and typically include atleast an amine, carbonyl, hydroxyl or carboxyl group, frequently atleast two of the functional chemical groups. The candidate agents oftencomprise cyclical carbon or heterocyclic structures and/or aromatic orpolyaromatic structures substituted with one or more of the abovefunctional groups. Candidate agents are also found among biomolecules,including peptides, polynucleotides, saccharides, fatty acids, steroids,purines, pyrimidines, derivatives, structural analogs or combinationsthereof.

Included are pharmacologically active drugs, genetically activemolecules, etc. Compounds of interest include chemotherapeutic agents,hormones or hormone antagonists, etc. Exemplary of pharmaceutical agentssuitable for this invention are those described in, “The PharmacologicalBasis of Therapeutics,” Goodman and Gilman, McGraw-Hill, New York, N.Y.,(1996), Ninth edition, under the sections: Water, Salts and Ions; DrugsAffecting Renal Function and Electrolyte Metabolism; Drugs AffectingGastrointestinal Function; Chemotherapy of Microbial Diseases;Chemotherapy of Neoplastic Diseases; Drugs Acting on Blood-Formingorgans; Hormones and Hormone Antagonists; Vitamins, Dermatology; andToxicology, all incorporated herein by reference. Also included aretoxins, and biological and chemical warfare agents, for example seeSomani, S. M. (Ed.), “Chemical Warfare Agents,” Academic Press, NewYork, 1992).

Test compounds include all of the classes of molecules described above,and may further comprise samples of unknown content. Of interest arecomplex mixtures of naturally occurring compounds derived from naturalsources such as plants. While many samples will comprise compounds insolution, solid samples that can be dissolved in a suitable solvent mayalso be assayed. Samples of interest include environmental samples, e.g.ground water, sea water, mining waste, etc.; biological samples, e.g.lysates prepared from crops, tissue samples, etc.; manufacturingsamples, e.g. time course during preparation of pharmaceuticals; as wellas libraries of compounds prepared for analysis; and the like. Samplesof interest include compounds being assessed for potential therapeuticvalue, i.e. drug candidates.

The term “samples” also includes the fluids described above to whichadditional components have been added, for example components thataffect the ionic strength, pH, total protein concentration, etc. Inaddition, the samples may be treated to achieve at least partialfractionation or concentration. Biological samples may be stored if careis taken to reduce degradation of the compound, e.g. under nitrogen,frozen, or a combination thereof. The volume of sample used issufficient to allow for measurable detection, usually from about 0.1 to1 ml of a biological sample is sufficient.

Compounds, including candidate agents, are obtained from a wide varietyof sources including libraries of synthetic or natural compounds. Forexample, numerous means are available for random and directed synthesisof a wide variety of organic compounds, including biomolecules,including expression of randomized oligonucleotides and oligopeptides.Alternatively, libraries of natural compounds in the form of bacterial,fungal, plant and animal extracts are available or readily produced.Additionally, natural or synthetically produced libraries and compoundsare readily modified through conventional chemical, physical andbiochemical means, and may be used to produce combinatorial libraries.Known pharmacological agents may be subjected to directed or randomchemical modifications, such as acylation, alkylation, esterification,amidification, etc. to produce structural analogs.

Agents are screened for biological activity by adding the agent to atleast one and usually a plurality of cell samples, usually inconjunction with cells lacking the agent. The change in parameters inresponse to the agent is measured, and the result evaluated bycomparison to reference cultures, e.g. in the presence and absence ofthe agent, obtained with other agents, etc.

The agents are conveniently added in solution, or readily soluble form,to the medium of cells in culture. The agents may be added in aflow-through system, as a stream, intermittent or continuous, oralternatively, adding a bolus of the compound, singly or incrementally,to an otherwise static solution. In a flow-through system, two fluidsare used, where one is a physiologically neutral solution, and the otheris the same solution with the test compound added. The first fluid ispassed over the cells, followed by the second. In a single solutionmethod, a bolus of the test compound is added to the volume of mediumsurrounding the cells. The overall concentrations of the components ofthe culture medium should not change significantly with the addition ofthe bolus, or between the two solutions in a flow through method.

Preferred agent formulations do not include additional components, suchas preservatives, that may have a significant effect on the overallformulation. Thus preferred formulations consist essentially of abiologically active compound and a physiologically acceptable carrier,e.g. water, ethanol, DMSO, etc. However, if a compound is liquid withouta solvent, the formulation may consist essentially of the compounditself.

A plurality of assays may be run in parallel with different agentconcentrations to obtain a differential response to the variousconcentrations. As known in the art, determining the effectiveconcentration of an agent typically uses a range of concentrationsresulting from 1:10, or other log scale, dilutions. The concentrationsmay be further refined with a second series of dilutions, if necessary.Typically, one of these concentrations serves as a negative control,i.e. at zero concentration or below the level of detection of the agentor at or below the concentration of agent that does not give adetectable change in the phenotype.

Various methods can be utilized for quantifying the presence of theselected markers. For measuring the amount of a molecule that ispresent, a convenient method is to label a molecule with a detectablemoiety, which may be fluorescent, luminescent, radioactive,enzymatically active, etc., particularly a molecule specific for bindingto the parameter with high affinity. Fluorescent moieties are readilyavailable for labeling virtually any biomolecule, structure, or celltype. Immunofluorescent moieties can be directed to bind not only tospecific proteins but also specific conformations, cleavage products, orsite modifications like phosphorylation. Individual peptides andproteins can be engineered to autofluoresce, e.g. by expressing them asgreen fluorescent protein chimeras inside cells (for a review see Joneset al. (1999) Trends Biotechnol. 17(12):477-81). Thus, antibodies can begenetically modified to provide a fluorescent dye as part of theirstructure. Depending upon the label chosen, parameters may be measuredusing other than fluorescent labels, using such immunoassay techniquesas radioimmunoassay (RIA) or enzyme linked immunosorbance assay (ELISA),homogeneous enzyme immunoassays, and related non-enzymatic techniques.The quantitation of nucleic acids, especially messenger RNAs, is also ofinterest as a parameter. These can be measured by hybridizationtechniques that depend on the sequence of nucleic acid nucleotides.Techniques include polymerase chain reaction methods as well as genearray techniques. See Current Protocols in Molecular Biology, Ausubel etal., eds, John Wiley & Sons, New York, N.Y., 2000; Freeman et al. (1999)Biotechniques 26(1):112-225; Kawamoto et al. (1999) Genome Res9(12):1305-12; and Chen et al. (1998) Genomics 51(3):313-24, forexamples.

Depletion of AMLSC

Depletion of AMLSC is useful in the treatment of AML. Depletion can beachieved by several methods. Depletion is defined as a reduction in thetarget population by up to about 30%, or up to about 40%, or up to about50%, or up to about 75% or more. An effective depletion is usuallydetermined by the sensitivity of the particular disease condition to thelevels of the target population. Thus in the treatment of certainconditions a depletion of even about 20% could be beneficial.

A marker-specific agent that specifically depletes the targeted AMLSC isused to contact the patient blood in vitro or in vivo, wherein after thecontacting step, there is a reduction in the number of viable AMLSC inthe targeted population. An exemplary agent for such purposes is anantibody that specifically binds to a marker or combination of markersof the present invention on the surface of the targeted AMLSC. Aneffective dose of antibodies for such a purpose is sufficient todecrease the targeted population to the desired level, for example asdescribed above. Antibodies for such purposes may have low antigenicityin humans or may be humanized antibodies.

In one embodiment of the invention, antibodies for depleting targetpopulation are added to patient blood in vivo. In another embodiment,the antibodies are added to the patient blood ex vivo. Beads coated withthe antibody of interest can be added to the blood, target cells boundto these beads can then be removed from the blood using procedurescommon in the art. In one embodiment the beads are magnetic and areremoved using a magnet. Alternatively, when the antibody isbiotinylated, it is also possible to indirectly immobilize the antibodyonto a solid phase which has adsorbed avidin, streptavidin, or the like.The solid phase, usually agarose or sepharose beads are separated fromthe blood by brief centrifugation. Multiple methods for taggingantibodies and removing such antibodies and any cells bound to theantibodies are routine in the art. Once the desired degree of depletionhas been achieved, the blood is returned to the patient. Depletion oftarget cells ex vivo decreases the side effects such as infusionreactions associated with the intravenous administration. An additionaladvantage is that the repertoire of available antibodies is expandedsignificantly as this procedure does not have to be limited toantibodies with low antigenicity in humans or humanized antibodies.

In some embodiments, the antibodies for depletion are bispecificantibodies. “Bispecific antibody” and “bispecific antibodies,” alsoknown as bifunctional antibodies, refers to antibodies that recognizetwo different antigens by virtue of possessing at least one firstantigen combining site specific for a first antigen or hapten, and atleast one second antigen combining site specific for a second antigen orhapten. Such antibodies can be produced by recombinant DNA methods orinclude, but are not limited to, antibodies produced chemically bymethods known in the art. Bispecific antibodies include all antibodiesor conjugates of antibodies, or polymeric forms of antibodies which arecapable of recognizing two different antigens. Bispecific antibodiesinclude antibodies that have been reduced and reformed so as to retaintheir bivalent characteristics and to antibodies that have beenchemically coupled so that they can have several antigen recognitionsites for each antigen.

Bispecific antibodies for use in the methods of the present inventionbind to at least one of the AMLSC antigens described herein, and maybind to two or more AMLSC antigens described herein. Antigencombinations of interest include, without limitation, CD47+CD96,CD47+CD99, CD47+Tim3, CD47+CD97, CD97+TIM3. In some embodiments, onespecificity of the antibody has a low affinity, e.g. less than about10⁻⁹ binding constant, usually less than about 10⁻⁸ binding constant,and may be more than about 10⁻⁷ binding constant.

Antibodies suitable for practicing the methods of the invention arepreferably monoclonal and multivalent, and may be human, humanized orchimeric antibodies, comprising single chain antibodies, Fab fragments,F(ab') fragments, fragments produced by a Fab expression library, and/orbinding fragments of any of the above. In certain embodiments of theinvention, the antibodies are human antigen-binding antibody fragmentsof the present invention and include, but are not limited to, Fab, Fab′and F(ab′)₂, Fd, single-chain Fvs (scFv), single-chain antibodies,disulfide-linked Fvs (sdFv) and fragments comprising either a V_(L) orV_(H) domain. Antigen-binding antibody fragments, including single-chainantibodies, may comprise the variable region(s) alone or in combinationwith the entirety or a portion of the following: hinge region, CH₁, CH₂,CH₃ and CL domains. Also included in the invention are antigen-bindingfragments comprising any combination of variable region(s) with a hingeregion, CH₁, CH₂, CH₃ and CL domains. Preferably, the antibodies arehuman, murine (e.g., mouse and rat), donkey, sheep, rabbit, goal, guineapig, camelid, horse, or chicken. As used herein, “human” antibodiesinclude antibodies having the amino acid sequence of a humanimmunoglobulin and include antibodies isolated from human immunoglobulinlibraries, from human B cells, or from animals transgenic for one ormore human immunoglobulins.

The antibodies suitable for practicing the methods of the presentinvention may be bispecific, trispecific or of greater multispecificity.Further, the antibodies of the present invention may have low risk oftoxicity against granulocyte (neutrophil), NK cells, and CD4⁺ cells asbystander cells.

Methods for making bispecific antibodies are known in the art.Traditional production of full length bispecific antibodies is based onthe coexpression of two immunoglobulin heavy chain-light chain pairs,where the two chains have different specificities (Millstein et al.,Nature, 305:537-539 (1983)). Because of the random assortment ofimmunoglobulin heavy and light chains, these hybridomas (quadromas)produce a potential mixture of 10 different antibody molecules, of whichonly one has the correct bispecific structure. Purification of thecorrect molecule, which is usually done by affinity chromatographysteps, is rather cumbersome, and the product yields are low. Similarprocedures are disclosed in WO 93/08829, and in Traunecker et al, EMBOJ., 10:3655-3659 (1991).

According to another approach described in WO96/27011, the interfacebetween a pair of antibody molecules can be engineered to maximize thepercentage of heterodimers which are recovered from recombinant cellculture. Such interfaces may comprise at least a part of the CH₃ domainof an antibody constant domain. In this method, one or more small aminoacid side chains from the interface of the first antibody molecule arereplaced with larger side chains (e.g., tyrosine or tryptophan).Compensatory “cavities” of identical or similar size to the large sidechain(s) are created on the interface of the second antibody molecule byreplacing large amino acid side chains with smaller ones (e.g., alanineor threonine). This provides a mechanism for increasing the yield of theheterodimer over other unwanted end-products such as homodimers. Analternative method links two different single chain variable regions toheat stable antigen (HSA). Using HSA as linker increases serum halflife, and has the benefit of low immunogenicity.

Bispecific antibodies include cross-linked or “heteroconjugate”antibodies. For example, one of the antibodies in the heteroconjugatecan be coupled to avidin, the other to biotin. Such antibodies have, forexample, been proposed to target immune system cells to unwanted cells(U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO91/00360, WO 92/200373, and EP 03089). Heteroconjugate antibodies may bemade using any convenient cross-linking methods. Suitable cross-linkingagents are well known in the art, and are disclosed in U.S. Pat. No.4,676,980, along with a number of cross-linking techniques.

Techniques for generating bispecific antibodies from antibody fragmentshave also been described in the literature. For example, bispecificantibodies can be prepared using chemical linkage. Brennan et al.,Science, 229:81 (1985) describe a procedure wherein intact antibodiesare proteolytically cleaved to generate F(ab')₂ fragments. Thesefragments are reduced in the presence of the dithiol complexing agentsodium arsenite to stabilize vicinal dithiols and prevent intermoleculardisulfide formation. The Fab′ fragments generated are then converted tothionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives isthen reconverted to the Fab′-thiol by reduction with mercaptoet-hylamineand is mixed with an equimolar amount of the other Fab′-TNB derivativeto form the bispecific antibody. The bispecific antibodies produced canbe used as agents for the selective immobilization of enzymes.

Various techniques for making and isolating bispecific antibodyfragments directly from recombinant cell culture have also beendescribed. For example, bispecific antibodies have been produced usingleucine zippers. Kos-telny et al., J. Immunol, 148(5):1547-1553 (1992).The leucine zipper peptides from the Fos and Jun proteins were linked tothe Fab′ portions of two different antibodies by gene fusion. Theantibody homodimers were reduced at the hinge region to form monomersand then re-oxidized to form the antibody heterodimers. This method canalso be utilized for the production of antibody homodimers. The“diabody” technology described by Hollinger et al., Proc. Natl. Acad.Sci. USA, 90:6444-6448 (1993) has provided an alternative mechanism formaking bispecific antibody fragments. The fragments comprise aheavy-chain variable domain (V_(H)) connected to a light-chain variabledomain (V_(L)) by a linker which is too short to allow pairing betweenthe two domains on the same chain. Accordingly, the V_(H) and V_(L)domains of one fragment are forced to pair with the complementary V_(L)and V_(H) domains of another fragment, thereby forming twoantigen-binding sites. Another strategy for making bispecific antibodyfragments by the use of single-chain Fv (sFv) dimers has also beenreported. See Gruber et al., J. Immunol., 152:5368 (1994).Alternatively, the antibodies can be “linear antibodies” as described inZapata et al. Protein Eng. 8(10): 1057-1062 (1995). Briefly, theseantibodies comprise a pair of tandem Fd segments (V_(H) -C_(H1)-V_(H)-C_(H)1) which form a pair of antigen binding regions. Linear antibodiescan be bispecific or monospecific.

Within the context of the present invention, antibodies are understoodto include monoclonal antibodies and polyclonal antibodies, antibodyfragments (e.g., Fab and F(ab′)₂), chimeric antibodies bifunctional orbispecific antibodies and tetrameric antibody complexes. Antibodies areunderstood to be reactive against a selected antigen on the surface of aT cell if they bind with an appropriate affinity (association constant),e.g. greater than or equal to 10⁷M⁻¹. Additionally, antibodies that maybe used in the methods of the present invention may also be described orspecified in terms of their binding affinities include those with adissociation constant or Kd less than 5×10⁻² M, 10⁻² M, 5×10⁻³ M, 10⁻³M, 5×10⁻⁴ M, 10⁻⁴ M, 5×10⁻⁵ M, 10⁻⁵ M, 5×10⁻⁸ M, 10⁻⁸M, 5×10⁻⁷ M, 10⁻⁷M, 5×10⁻⁸ M, 10⁻⁸ M, 5×10⁻⁹ M, 10⁻⁹ M, 5×10⁻10 _(M,) 10⁻⁹ M, 5×10⁻¹¹ M,10¹¹ M, 5×10⁻¹² M, 10⁻¹² M, 5×10⁻¹³ M, 10¹³ M, 5×10⁻¹⁴ M, 10¹⁴ M,5×10⁻¹⁵ M, 10⁻¹⁵ M.

Antibodies can be fragmented using conventional techniques and thefragments screened for utility in the same manner as described above forthe whole antibodies. For example, F(ab′)₂ fragments can be generated bytreating antibody with pepsin. The resulting F(ab′)₂ fragment can betreated to reduce disulfide bridges to produce Fab′ fragments.

The invention also contemplates chimeric antibody derivatives, i.e.,antibody molecules that combine a non-human animal variable region and ahuman constant region. Chimeric antibody molecules can include, forexample, the antigen binding domain from an antibody of a mouse, rat, orother species, with human constant regions. A variety of approaches formaking chimeric antibodies have been described and can be used to makechimeric antibodies containing the immunoglobulin variable region whichrecognizes the selected antigens on the surface of differentiated cellsor tumor cells. See, for example, Morrison et al., 1985; Proc. Natl.Acad. Sci. U.S.A. 81,6851; Takeda et al., 1985, Nature 314:452; Cabillyet al., U.S. Pat. No. 4,816,567; Boss et al., U.S. Pat. No. 4,816,397;Tanaguchi et al., European Patent Publication EP171496; European PatentPublication 0173494, United Kingdom patent GB 2177096B.

Chemical conjugation is based on the use of homo- and heterobifunctionalreagents with E-amino groups or hinge region thiol groups.Homobifunctional reagents such as 5,5′-Dithiobis(2-nitrobenzoicacid)(DNTB) generate disulfide bonds between the two Fabs, and0-phenylenedimaleimide (O-PDM) generate thioether bonds between the twoFabs (Brenner et al., 1985, Glennie et al., 1987). Heterobifunctionalreagents such as N-succinimidyl-3-(2-pyridylditio)propionate (SPDP)combine exposed amino groups of antibodies and Fab fragments, regardlessof class or isotype (Van Dijk et al., 1989).

The antibodies of the invention, i.e., antibodies that are useful fortreating cancers, as well as other cancer comprising cancer stem cellsexpressing antigens set forth in Table 1, include derivatives that aremodified, i.e., by the covalent attachment of any type of molecule tothe antibody such that covalent attachment does not prevent the antibodyfrom binding to the antigens. For example, but not by way of limitation,the antibody derivatives include antibodies that have been modified,e.g., by glycosylation, acetylation, pegylation, phosphorylation,amidation, derivatization by known protecting/blocking groups,proteolytic cleavage, linkage to a cellular ligand or other protein,etc. Any of numerous chemical modifications may be carried out by knowntechniques, including, but not limited to specific chemical cleavage,acetylation, formylation, metabolic synthesis of tunicamycin, etc.Additionally, the derivative may contain one or more non-classical aminoacids.

Kits may be provided, where the kit will comprise staining reagents thatare sufficient to differentially identify the AMLSC described herein. Acombination of interest may include one or more reagents specific for amarker or combination of markers of the present invention, and mayfurther include antibodies specific for CD96, CD34, and CD38. Thestaining reagents are preferably antibodies, and may be detectablylabeled. Kits may also include tubes, buffers, etc., and instructionsfor use.

Each publication cited in this specification is hereby incorporated byreference in its entirety for all purposes.

It is to be understood that this invention is not limited to theparticular methodology, protocols, cell lines, animal species or genera,and reagents described, as such may vary. It is also to be understoodthat the terminology used herein is for the purpose of describingparticular embodiments only, and is not intended to limit the scope ofthe present invention, which will be limited only by the appendedclaims.

As used herein the singular forms “a”, “and”, and “the” include pluralreferents unless the context clearly dictates otherwise. Thus, forexample, reference to “a cell” includes a plurality of such cells andreference to “the culture” includes reference to one or more culturesand equivalents thereof known to those skilled in the art, and so forth.All technical and scientific terms used herein have the same meaning ascommonly understood to one of ordinary skill in the art to which thisinvention belongs unless clearly indicated otherwise.

EXPERIMENTAL Example 1 Identification of Cell Surface MoleculesPreferentially Expressed on Human Acute Myeloid Leukemia Stem CellsCompared to Their Normal Counterparts

Prospective Identification of a Human Multipotent Progenitor, the Cellof Origin for AML LSC. Identification of cell surface molecules that arepreferentially expressed on AML LSC would be greatly facilitated bydetermining the cell within the normal hematopoietic hierarchy thatundergoes transformation to become an AML LSC. The prevailing view inthe field has been that AML LSC arise out of hematopoietic stem cells(HSC), since both stem cell populations are enriched in Lin-CD34+CD38−cells. However, human HSC have been shown to express CD90, while AML LSCare CD90−. Furthermore, HSC from long-term remission t(8;21) AMLpatients were found to contain the AML1-ETO translocation product,suggesting that the HSC were pre-leukemic, and that full transformationto AML LSC occurred in a downstream progenitor.

While it is certainly possible that HSC are in fact the cell of originfor AML LSC, and that these cells lose expression of CD90 as aconsequence of transformation, it is also possible that AML LSCoriginate from downstream Lin-CD34+CD38-CD90− cells. We utilized aNOD/SCID/IL-2R gamma null (NOG) newborn xenotransplantation model toassay the function of subpopulations of Lin-CD34+CD38− cord blood,identified on the basis of CD90 and CD45RA expression.Lin-CD34+CD38-CD90+ cells produced long-term multi-lineage engraftmentand formed successful secondary transplants, and therefore containedHSC. Transplantation of purified Lin-CD34+CD38-CD90-CD45RA− cellsresulted in lower levels of multi-lineage engraftment in primaryrecipients, and a statistically significant reduced ability to formlong-term secondary transplants. In fact, with transplantation of 50purified cells, these cells failed to long-term engraft, unlike theLin-CD34+CD38-CD90+ HSC. Thus, Lin-CD34+CD38-CD9O-CD45RA− cells aremultipotent and possess limited self-renewal ability. These cells aretermed multipotent progenitors (MPP) and represent the possible cell oforigin of AML LSC.

Use of Gene Expression Profiling to Identify Cell Surface MoleculesPreferentially Expressed on AML LSC Compared to Their NormalCounterparts, HSC and MPP. Cell surface molecules preferentiallyexpressed on human acute myeloid leukemia stem cells (AML LSC) comparedto their normal counterparts have therapeutic applications outlinedbelow. One strategy to identify such molecules has been to generate geneexpression profiles of AML LSC and normal HSC and MPP, and compare themfor differentially expressed genes.

Normal bone marrow HSC and MPP (n=4) and AML LSC (n=9) were purified byFACS. Total RNA was prepared, amplified, and hybridized to Affymetrixhuman DNA microarrays. Statistical analysis identified 4037 genesdifferentially expressed between HSC and LSC, and 4208 genesdifferentially expressed between MPP and LSC, with p<0.05 and a FalseDiscovery Rate of 5% (FIG. 1A). Investigation of these differentiallyexpressed genes identified 288 and 318 cell surface moleculespreferentially expressed in AML LSC by at least 2-fold compared to HSCand MPP, respectively. Selected members of this list, including manywith the greatest preferential expression in AML LSC are indicated (FIG.1B, Table 1).

TABLE 1 Fold Change Genbank Gene Symbol Description 94.34 M27331 TRGC2 Tcell receptor gamma constant 2 57.47 NM_005816 CD96 CD96 antigen 47.17AI862120 MAMDC2 MAM domain containing 2 32.36 AF348078 SUCNR1 succinatereceptor 1 32.05 M16768 TRGC2 T cell receptor gamma constant 2 30.96NM_002182 IL1RAP interleukin 1 receptor accessory protein 29.85 M13231TRGC2 T cell receptor gamma constant 2 27.55 NM_003332 TYROBP TYROprotein tyrosine kinase binding protein 26.88 NM_004271 LY86 lymphocyteantigen 86 20.96 NM_014879 P2RY14 purinergic receptor P2Y, G-proteincoupled, 14 18.38 BC020749 CD96 CD96 antigen 18.38 NM_005048 PTHR2parathyroid hormone receptor 2 17.73 AI625747 ADRB1 Adrenergic, beta-1-,receptor 17.36 NM_015376 RASGRP3 RAS guanyl releasing protein 3 (calciumand DAG- regulated) 16.84 U62027 C3AR1 complement component 3a receptor1 14.49 AW025572 HAVCR2 hepatitis A virus cellular receptor 2 12.48AF285447 HCST hematopoietic cell signal transducer 11.92 AI805323 LGR7leucine-rich repeat-containing G protein-coupled receptor 7 11.67NM_001197 BIK BCL2-interacting killer (apoptosis-inducing) 11.53NM_018092 NETO2 neuropilin (NRP) and tolloid (TLL)-like 2 11.07 N74607AQP3 aquaporin 3 10.88 BF439675 CD69 CD69 antigen (p60, early T-cellactivation antigen) 10.48 NM_001769 CD9 CD9 antigen (p24) 10.32 AF167343IL1RAP interleukin 1 receptor accessory protein 9.52 AA814140 C5orf18chromosome 5 open reading frame 18 8.77 NM_005582 CD180 CD180 antigen7.46 AF039686 GPR34 G protein-coupled receptor 34 7.30 AI056776 ITGA6Integrin, alpha 6 7.19 AJ277151 TNFRSF4 tumor necrosis factor receptorsuperfamily, member 4 6.99 AI738675 SELPLG Selectin P ligand 6.85AA888858 PDE3B Phosphodiesterase 3B, cGMP-inhibited 6.80 AU149572 ADCY2adenylate cyclase 2 (brain) 6.80 NM_002299 LCT lactase 6.58 NM_005296GPR23 G protein-coupled receptor 23 6.45 NM_004106 FCER1G Fc fragment ofIgE, high affinity receptor 6.29 AI741056 SELPLG selectin P ligand 6.25AW406569 MGC15619 6.06 M81695 ITGAX integrin, alpha X 5.92 NM_003494DYSF dysferlin 5.85 AI860212 PAG1 phosphoprotein associated withglycosphingolipid microdomains 1 5.75 NM_013447 EMR2 egf-like modulecontaining, mucin-like, hormone receptor-like 2 5.62 NM_017806 LIME1 Lckinteracting transmembrane adaptor 1 5.62 AK092824 AMN Amnionless homolog(mouse) 5.59 AF345567 GPR174 G protein-coupled receptor 174 5.29BC041928 IL1RAP Interleukin 1 receptor accessory protein 5.26 L03419FCGR1A Fc fragment of IgG, high affinity Ia, receptor (CD64); Fc-gammareceptor I B2 5.24 BG230586 SLC7A6 solute carrier family 7 (cationicamino acid transporter, y+ system), member 6 5.18 AF015524 CCRL2chemokine (C-C motif) receptor-like 2 5.13 AA631143 SLC45A3 solutecarrier family 45, member 3 5.10 AJ240085 TRAT1 T cell receptorassociated transmembrane adaptor 1 5.05 AW183080 GPR92 G protein-coupledreceptor 92 5.03 NM_002120 HLA-DOB major histocompatibility complex,class II, DO beta 5.03 NM_015364 LY96 lymphocyte antigen 96 4.90NM_020399 GOPC golgi associated PDZ and coiled-coil motif containing4.88 AK026133 SEMA4B semaphorin 4.88 BC041664 VMD2 vitelliform maculardystrophy 2 4.85 NM_152592 C14orf49 chromosome 14 open reading frame 494.85 AA923524 RASGRP4 RAS guanyl releasing protein 4 4.85 BC008777 ITGALintegrin, alpha L) 4.67 AF014403 PPAP2A phosphatidic acid phosphatasetype 2A 4.65 AK097698 SORCS2 Sortilin-related VPS10 domain containingreceptor 2 4.63 X14355 FCGR1A Fc fragment of IgG, high affinity Ia,receptor (CD64) 4.55 NM_001629 ALOX5AP arachidonate5-lipoxygenase-activating protein 4.50 AU155968 C18orf1 chromosome 18open reading frame 1 4.44 AK075092 HERV-FRD HERV-FRD provirus ancestralEnv polyprotein 4.42 NM_020960 GPR107 G protein-coupled receptor 1074.37 BC000039 FAM26B family with sequence similarity 26, member B 4.35NM_153701 IL12RB1 interleukin 12 receptor, beta 1 4.35 AI762344 PTGER1prostaglandin E receptor 1 (subtype EP1), 42 kDa 4.31 NM_006459 SPFH1SPFH domain family, member 1 4.27 NM_003126 SPTA1 spectrin, alpha,erythrocytic 1 (elliptocytosis 2) 4.22 AL518391 AQP1 aquaporin 1(channel-forming integral protein, 28 kDa) 4.12 AK026188 PCDHGC3protocadherin gamma subfamily C 4.10 AU146685 EDG2 Endothelialdifferentiation, lysophosphatidic acid G- protein-coupled receptor, 24.05 BE673587 SLC14A1 Solute carrier family 14 (urea transporter),member 1 (Kidd blood group) 4.02 BF129969 TSPAN2 tetraspanin 2 4.00AW243272 KCNK5 Potassium channel, subfamily K, member 5 3.98 T68858DHRS3 Dehydrogenase/reductase (SDR family) member 3 3.94 AI827849 VTI1AVesicle transport through interaction with t-SNAREs homolog 1A (yeast)3.86 AL134012 NRXN2 Neurexin 2 3.83 BG230614 CD47 CD47 antigen 3.80AI869717 MGC15523 MGC15523 3.80 AI458583 SIMP Source of immunodominantMHC-associated peptides 3.79 NM_002183 IL3RA interleukin 3 receptor,alpha (low affinity) 3.79 AA608820 NRXN2 neurexin 2 3.73 NM_000206 IL2RGinterleukin 2 receptor 3.72 BC002737 VAMP2 synaptobrevin 2 3.72 BC005884BID BH3 interacting domain death agonist; BH3 interacting domain deathagonist 3.68 AI688418 PLXNA2 plexin A2 3.68 BC003105 PTP4A3 proteintyrosine phosphatase type IVA, member 3 3.68 NM_001772 CD33 CD33 antigen(gp67) 3.65 BC007524 SPAG9 sperm associated antigen 9 3.64 AI344200SLC25A35 solute carrier family 25, member 35 3.64 BC005253 KLHL20kelch-like 20 (Drosophila) 3.60 AI335263 NETO2 neuropilin (NRP) andtolloid (TLL)-like 2 3.58 BF381837 C20orf52 chromosome 20 open readingframe 52 3.51 NM_002886 RAP2A RAP2A 3.50 NM_007063 TBC1D8 TBC1 domainfamily, member 8 (with GRAM domain) 3.45 AK027160 BCL2L11 BCL2-like 11(apoptosis facilitator) 3.44 BF055366 EDG2 endothelial differentiation,lysophosphatidic acid G- protein-coupled receptor, 2 3.42 NM_003608GPR65 G protein-coupled receptor 65 3.41 AI675453 PLXNA3 plexin A3 3.40AV734194 DPP8 dipeptidylpeptidase 8 3.38 BC000232 C5orf18 chromosome 5open reading frame 18 3.36 BC001956 KIAA1961 KIAA1961 gene 3.34NM_013332 HIG2 hypoxia-inducible protein 2 3.31 BC029450 SLC33A1 Solutecarrier family 33 (acetyl-CoA transporter), member 1 3.30 AW008505C18orf1 chromosome 18 open reading frame 1 3.29 BF693956 CD47 CD47antigen 3.28 BF677986 KIAA1961 KIAA1961 gene 3.27 AI433691 CACNA2D4calcium channel, voltage-dependent, alpha 2/delta subunit 4 3.26AB014573 NPHP4 nephronophthisis 4 3.25 AL582804 LY9 lymphocyte antigen 93.25 BG236280 CD86 CD86 antigen 3.24 AA639289 SLC26A7 Solute carrierfamily 26, member 7 3.24 NM_005211 CSF1R colony stimulating factor 1receptor 3.24 AI051254 TRPM2 transient receptor potential cationchannel, subfamily M, member 2 3.23 AW292816 ABHD2 abhydrolase domaincontaining 2 3.23 BC040275 RASGRF1 Ras protein-specific guaninenucleotide-releasing factor 1 3.22 NM_021911 GABRB2 gamma-aminobutyricacid (GABA) A receptor, beta 2 3.19 AI660619 SLC7A6 solute carrierfamily 7 (cationic amino acid transporter, y+ system), member 6 3.19NM_001860 SLC31A2 solute carrier family 31 (copper transporters), member2 3.18 NM_015680 C2orf24 chromosome 2 open reading frame 24 3.17AW058600 SLC36A1 solute carrier family 36 3.16 AU145049 HIP1 Huntingtininteracting protein 1 3.15 NM_005770 SERF2 small EDRK-rich factor 2 3.15NM_003566 EEA1 Early endosome antigen 1, 162 kD 3.14 NM_020041 SLC2A9solute carrier family 2 (facilitated glucose transporter), member 9 3.14W90718 SLC24A4 solute carrier family 24 3.13 AI423165 TICAM2 toll-likereceptor adaptor molecule 2 3.12 AI674647 SPPL2A signal peptidepeptidase-like 2A 3.11 NM_004121 GGTLA1 gamma-glutamyltransferase-likeactivity 1 3.10 NM_004546 NDUFB2 NADH dehydrogenase (ubiquinone) 1 betasubcomplex, 2, 8 kDa 3.05 X15786 RET ret proto-oncogene (multipleendocrine neoplasia and medullary thyroid carcinoma 1, Hirschsprungdisease) 3.05 AF181660 MPZL1 myelin protein zero-like 1 3.05 BG230614CD47 CD47 antigen (Rh-related antigen, integrin- associated signaltransducer) 3.00 AI571996 STAM2 signal transducing adaptor molecule (SH3domain and ITAM motif) 2 2.99 NM_000201 ICAM1 intercellular adhesionmolecule 1 (CD54), human rhinovirus receptor 2.93 NM_025244 TSGA10testis specific, 10 2.93 AU147538 PRKCE Protein kinase C, epsilon 2.92NM_024576 OGFRL1 opioid growth factor receptor-like 1 2.91 AI248055ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP), member 4 2.86AA503877 CEPT1 Choline/ethanolamine phosphotransferase 1 2.84 BC030993FLJ21127 Hypothetical protein FLJ21127 2.82 AA829818 LY86 Lymphocyteantigen 86 2.82 NM_001859 SLC31A1 solute carrier family 31 (coppertransporters), member 1 2.81 M74721 CD79A CD79A antigen(immunoglobulin-associated alpha) 2.79 AI986112 MGAT4B Mannosyl(alpha-1,3-)-glycoprotein beta-1,4-N- acetylglucosaminyltransferase,isoenzyme B 2.79 NM_030930 UNC93B1 unc-93 homolog B1 (C. elegans);unc-93 homolog B1 (C. elegans) 2.79 X74039 PLAUR plasminogen activator,urokinase receptor 2.78 BF514291 LY86 Lymphocyte antigen 86 2.75BC005253 KLHL20 kelch-like 20 (Drosophila) 2.73 AB036432 AGER advancedglycosylation end product-specific receptor 2.71 NM_007245 ATXN2L ataxin2-like 2.71 NM_016072 GOLT1B golgi transport 1 homolog B (S. cerevisiae)2.71 AI453548 ZDHHC8 zinc finger, DHHC-type containing 8 2.70 AI636233TMEM8 transmembrane protein 8 (five membrane-spanning domains) 2.69BE502509 T3JAM TRAF3 interacting protein 3 2.69 AW117765 PEX13peroxisome biogenesis factor 13 2.69 AW052216 IL17RB Interleukin 17receptor B 2.67 NM_003853 IL18RAP interleukin 18 receptor accessoryprotein 2.66 NM_002490 NDUFA6 NADH dehydrogenase (ubiquinone) 1 alphasubcomplex, 6, 14 kDa 2.65 NM_016639 TNFRSF12A tumor necrosis factorreceptor superfamily, member 12A 2.65 AI363185 FLJ20255 Hypotheticalprotein FLJ20255 2.65 NM_052931 SLAMF6 SLAM family member 6 2.65AW571669 TNFRSF19L tumor necrosis factor receptor superfamily, member19-like 2.64 AA654142 CEECAM1 cerebral endothelial cell adhesionmolecule 1 2.62 AW510783 TMEM63A transmembrane protein 63A 2.61 W95007ACSL4 Acyl-CoA synthetase long-chain family member 4 2.60 S76475 NTRK3neurotrophic tyrosine kinase, receptor, type 3 2.60 AJ130713 SIGLEC7sialic acid binding Ig-like lectin 7 2.56 NM_003775 EDG6 endothelialdifferentiation, G-protein-coupled receptor 6 2.55 AI978986 MAMDC4 MAMdomain containing 4 2.54 AF010447 MR1 major histocompatibility complex,class I-related 2.54 NM_006068 TLR6 toll-like receptor 6 2.53 AF041811NTRK3 neurotrophic tyrosine kinase, receptor, type 3 2.53 AW953521SERF2; HYPK small EDRK-rich factor 2; Huntingtin interacting protein K2.51 AW293276 CD53 CD53 antigen 2.49 AK023058 PLXNA2 Plexin A2 2.49AI125204 C6orf128 chromosome 6 open reading frame 128 2.49 NM_000392ABCC2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 2.46BC032474 TIRAP toll-interleukin 1 receptor (TIR) domain containingadaptor protein 2.44 NM_031211 IMAA SLC7A5 pseudogene 2.44 AI797836 CD5CD5 antigen (p56-62) 2.41 W72082 C1QR1 complement component 1 2.40AA708616 DPP9 dipeptidylpeptidase 9 2.40 BM987094 DLGAP4 discs, large(Drosophila) homolog-associated protein 4 2.40 AL713719 LOC283501ATPase, Class VI, type 11A 2.39 AI628734 PRLR prolactin receptor 2.39NM_012110 CHIC2 cysteine-rich hydrophobic domain 2 2.38 AK022002 TFR2transferrin receptor 2 2.37 NM_001555 IGSF1 immunoglobulin superfamily,member 1 2.36 AA426091 C19orf15 chromosome 19 open reading frame 15 2.36BE547542 GOPC golgi associated PDZ and coiled-coil motif containing 2.36NM_004231 ATP6V1F ATPase, H+ transporting, lysosomal 14 kDa, V1 subunitF 2.36 AJ130712 SIGLEC7 sialic acid binding Ig-like lectin 7 2.36NM_017905 TMCO3 transmembrane and coiled-coil domains 3 2.35 AB054985CACNB1 calcium channel, voltage-dependent, beta 1 subunit 2.35 NM_005003NDUFAB1 NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa 2.35 NM_001251 CD68 CD68 antigen 2.35 AA700869 PSCD2 Pleckstrinhomology, Sec7 and coiled-coil domains 2 (cytohesin-2) 2.35 U94903 CD44CD44 antigen (homing function and Indian blood group system) 2.35NM_003841 TNFRSF10C tumor necrosis factor receptor superfamily, member10c, decoy without an intracellular domain 2.33 NM_004541 NDUFA1 NADHdehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5 kDa 2.33 BE567130KLRK1 Killer cell lectin-like receptor subfamily K, member 1 2.31NM_017460 CYP3A4 cytochrome P450, family 3, subfamily A, polypeptide 42.31 AI339536 DSC1 Desmocollin 1 2.31 NM_001783 CD79A CD79A antigen(immunoglobulin-associated alpha); CD79A antigen(immunoglobulin-associated alpha) 2.30 AA333161 VTI1A vesicle transportthrough interaction with t-SNAREs homolog 1A (yeast) 2.30 AW134823 CD6CD6 antigen; CD6 antigen 2.30 AL137537 ATP8B2 ATPase, Class I, type 8B,member 2 2.29 AI671983 SLC2A9 solute carrier family 2 (facilitatedglucose transporter), member 9 2.29 AA018187 C22orf3 chromosome 22 openreading frame 3 2.29 AL117415 ADAM33 ADAM metallopeptidase domain 332.29 NM_002588 PCDHGC3 protocadherin gamma subfamily C 2.29 NM_020960GPR107 G protein-coupled receptor 107 2.29 AK074635 GENX-3414 Genethonin1 2.29 BE138575 ITGB5 Integrin, beta 5 2.28 NM_003830 SIGLEC5 sialicacid binding Ig-like lectin 5; sialic acid binding Ig-like lectin 5 2.28NM_013319 UBIAD1 UbiA prenyltransferase domain containing 1 2.28 M63889FGFR1 fibroblast growth factor receptor 1 (fms-related tyrosine kinase2, Pfeiffer syndrome) 2.27 H67156 MSCP Solute carrier family 25, member37 2.27 BC006215 SMEK2 KIAA1387 protein; KIAA1387 protein 2.27 AL109653SLITRK2 SLIT and NTRK-like family, member 2 2.27 NM_007011 ABHD2abhydrolase domain containing 2 2.26 AI767210 MGC11332 Hypotheticalprotein MGC11332 2.26 BF723605 NRCAM Neuronal cell adhesion molecule2.26 R08129 CDA08 T-cell immunomodulatory protein 2.26 AF052059 SEL1Lsel-1 suppressor of lin-12-like (C. elegans) 2.26 NM_005729 PPIFpeptidylprolyl isomerase F (cyclophilin F) 2.25 BE858032 ARL2L1ADP-ribosylation factor-like 2-like 1 2.25 AI950390 C14orf118 Chromosome14 open reading frame 118 2.24 NM_017767 SLC39A4 solute carrier family39 (zinc transporter), member 4 2.24 AL110273 SPTAN1 Spectrin, alpha,non-erythrocytic 1 (alpha-fodrin) 2.24 AI077660 CDA08 T-cellimmunomodulatory protein 2.23 AA488687 SLC7A11 solute carrier family 7,(cationic amino acid transporter, y+ system) member 11 2.23 NM_000634IL8RA interleukin 8 receptor, alpha 2.22 AL390177 MGC34032 Solutecarrier family 44, member 5 2.21 NM_001531 MR1 major histocompatibilitycomplex, class I-related 2.21 NM_003183 ADAM17 ADAM metallopeptidasedomain 17 (tumor necrosis factor, alpha, converting enzyme) 2.20AC003999 SCAP2 src family associated phosphoprotein 2 2.20 BC014416SLC33A1 solute carrier family 33 (acetyl-CoA transporter), member 1 2.20AF226731 ADORA3 adenosine A3 receptor 2.19 AI608725 ICAM1 intercellularadhesion molecule 1 (CD54), human rhinovirus receptor 2.19 U41163SLC6A8; solute carrier family 6 (neurotransmitter transporter, FLJ43855creatine), member 8; similar to sodium- and chloride- dependent creatinetransporter 2.19 AU147799 LRRC15 leucine rich repeat containing 15 2.18AW337166 LOC255104 Transmembrane and coiled-coil domains 4 2.18NM_006505 PVR poliovirus receptor 2.18 AI638420 CLIC4 chlorideintracellular channel 4 2.18 AI167482 SCUBE3 Signal peptide, CUB domain,EGF-like 3 2.18 AI739514 HAS3 hyaluronan synthase 3 2.18 NM_005971 FXYD3FXYD domain containing ion transport regulator 3 2.17 AL022398 TRAF3IP3TRAF3 interacting protein 3 2.17 U90940 FCGR2C Fc fragment of IgG, lowaffinity IIc, receptor for (CD32) 2.16 BC023540 SORCS1 Sortilin-relatedVPS10 domain containing receptor 1 2.16 AV713913 OSTM1 osteopetrosisassociated transmembrane protein 1 2.15 NM_024505 NOX5 NADPH oxidase,EF-hand calcium binding domain 5 2.15 BC006178 SEC22L3 SEC22 vesicletrafficking protein-like 3 (S. cerevisiae); SEC22 vesicle traffickingprotein-like 3 (S. cerevisiae) 2.15 BG151527 GRIK5 glutamate receptor,ionotropic, kainate 5 2.14 AW001754 NEGR1 neuronal growth regulator 12.14 NM_013979 BNIP1 BCL2/adenovirus E1B 19 kDa interacting protein 12.14 NM_018643 TREM1 triggering receptor expressed on myeloid cells 12.12 NM_005284 GPR6 G protein-coupled receptor 6 2.11 AA454190 ZDHHC20zinc finger, DHHC-type containing 20 2.11 AB048796 TMPRSS13transmembrane protease, serine 13 2.11 AL044520 NYD-SP21 testesdevelopment-related NYD-SP21 2.11 BE463930 TMAP1 Matrix-remodellingassociated 7 2.10 NM_152264 SLC39A13 solute carrier family 39 (zinctransporter), member 13 2.08 AL530874 EPHB2 EPH receptor B2 2.07NM_018668 VPS33B vacuolar protein sorting 33B (yeast) 2.07 NM_024531GPR172A G protein-coupled receptor 172A 2.07 NM_023038 ADAM19 ADAMmetallopeptidase domain 19 (meltrin beta) 2.07 BC001281 TNFRSF10B tumornecrosis factor receptor super-family, member 10b 2.07 AF217749 PCDHB9protocadherin beta 9 2.06 AB030077 FGFR2 fibroblast growth factorreceptor 2 (bacteria- expressed kinase, keratinocyte growth factorreceptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffersyndrome, Jackson-Weiss syndrome) 2.06 AL137432 SUSD1 sushi domaincontaining 1 2.05 NM_004518 KCNQ2 potassium voltage-gated channel,KQT-like subfamily, member 2 2.04 AI672363 VPS33B vacuolar proteinsorting 33B (yeast) 2.04 NM_006671 SLC1A7 solute carrier family 1(glutamate transporter), member 7 2.03 AA215519 DLGAP1 Discs, large(Drosophila) homolog-associated protein 1 2.02 NM_004648 PTPNS1 proteintyrosine phosphatase, non-receptor type substrate 1 2.02 NM_002564 P2RY2purinergic receptor P2Y, G-protein coupled, 2 2.01 BF511678 SCUBE3Signal peptide, CUB domain, EGF-like 3 2.01 BC013385 CLEC7A C-typelectin domain family 7, member A

TABLE 2 Fold Change Genbank Gene Symbol Description 57.47 NM_005816 CD96CD96 antigen 32.36 AF348078 SUCNR1 succinate receptor 1 30.96 NM_002182IL1RAP interleukin 1 receptor accessory protein 27.55 NM_003332 TYROBPTYRO protein tyrosine kinase binding protein 26.88 NM_004271 LY86lymphocyte antigen 86 20.96 NM_014879 P2RY14 purinergic receptor P2Y,G-protein coupled, 14 18.38 NM_005048 PTHR2 parathyroid hormone receptor2 17.73 AI625747 ADRB1 Adrenergic, beta-1-, receptor 17.36 NM_015376RASGRP3 RAS guanyl releasing protein 3 (calcium and DAG-regulated) 16.84U62027 C3AR1 complement component 3a receptor 1 14.49 AW025572 HAVCR2hepatitis A virus cellular receptor 2 12.48 AF285447 HCST hematopoieticcell signal transducer 11.92 AI805323 LGR7 leucine-richrepeat-containing G protein-coupled receptor 7 11.67 NM_001197 BIKBCL2-interacting killer (apoptosis-inducing) 11.53 NM_018092 NETO2neuropilin (NRP) and tolloid (TLL)-like 2 11.07 N74607 AQP3 aquaporin 310.48 NM_001769 CD9 CD9 antigen (p24) 8.77 NM_005582 CD180 CD180 antigen7.46 AF039686 GPR34 G protein-coupled receptor 34 7.19 AJ277151 TNFRSF4tumor necrosis factor receptor superfamily, member 4 6.85 AA888858 PDE3BPhosphodiesterase 3B, cGMP-inhibited 6.80 AU149572 ADCY2 adenylatecyclase 2 (brain) 6.80 NM_002299 LCT lactase 6.58 NM_005296 GPR23 Gprotein-coupled receptor 23 6.45 NM_004106 FCER1G Fc fragment of IgE,high affinity I, receptor for; gamma polypeptide 6.25 AW406569 MGC15619hypothetical protein MGC15619 6.06 M81695 ITGAX integrin, alpha X(antigen CD11C (p150), alpha polypeptide) 5.92 NM_003494 DYSF dysferlin,limb girdle muscular dystrophy 2B (autosomal recessive) 5.75 NM_013447EMR2 egf-like module containing, mucin-like, hormone receptor-like 25.62 NM_017806 LIME1 Lck interacting transmembrane adaptor 1 5.62AK092824 AMN Amnionless homolog (mouse) 5.59 AF345567 GPR174 Gprotein-coupled receptor 174 5.26 L03419 FCGR1A; Fc fragment of IgG,high affinity Ia, receptor LOC440607 (CD64); Fc-gamma receptor I B2 5.18AF015524 CCRL2 chemokine (C-C motif) receptor-like 2 5.13 AA631143SLC45A3 solute carrier family 45, member 3 5.10 AJ240085 TRAT1 T cellreceptor associated transmembrane adaptor 1 5.05 AW183080 GPR92 Gprotein-coupled receptor 92 5.03 NM_002120 HLA-DOB majorhistocompatibility complex, class II, DO beta 5.03 NM_015364 LY96lymphocyte antigen 96

TABLE 3 Fold Change Genbank Gene Symbol Description 57.47 NM_005816 CD96CD96 antigen 32.36 AF348078 SUCNR1 succinate receptor 1 30.96 NM_002182IL1RAP interleukin 1 receptor accessory protein 27.55 NM_003332 TYROBPTYRO protein tyrosine kinase binding protein 26.88 NM_004271 LY86lymphocyte antigen 86 20.96 NM_014879 P2RY14 purinergic receptor P2Y,G-protein coupled, 14 18.38 NM_005048 PTHR2 parathyroid hormone receptor2 17.73 AI625747 ADRB1 Adrenergic, beta-1-, receptor 17.36 NM_015376RASGRP3 RAS guanyl releasing protein 3 (calcium and DAG-regulated) 16.84U62027 C3AR1 complement component 3a receptor 1 14.49 AW025572 HAVCR2hepatitis A virus cellular receptor 2 12.48 AF285447 HCST hematopoieticcell signal transducer 11.92 AI805323 LGR7 leucine-richrepeat-containing G protein-coupled receptor 7 11.67 NM_001197 BIKBCL2-interacting killer (apoptosis-inducing) 11.53 NM_018092 NETO2neuropilin (NRP) and tolloid (TLL)-like 2 11.07 N74607 AQP3 aquaporin 310.88 BF439675 CD69 CD69 antigen (p60, early T-cell activation antigen)10.48 NM_001769 CD9 CD9 antigen (p24) 9.52 AA814140 C5orf18 chromosome 5open reading frame 18 8.77 NM_005582 CD180 CD180 antigen 7.46 AF039686GPR34 G protein-coupled receptor 34 7.30 AI056776 ITGA6 Integrin, alpha6 7.19 AJ277151 TNFRSF4 tumor necrosis factor receptor superfamily,member 4 6.99 AI738675 SELPLG Selectin P ligand 6.85 AA888858 PDE3BPhosphodiesterase 3B, cGMP-inhibited 6.80 AU149572 ADCY2 adenylatecyclase 2 (brain) 6.80 NM_002299 LCT lactase 6.58 NM_005296 GPR23 Gprotein-coupled receptor 23 6.45 NM_004106 FCER1G Fc fragment of IgE,high affinity I, receptor for; gamma polypeptide 6.25 AW406569 MGC15619hypothetical protein MGC15619 6.06 M81695 ITGAX integrin, alpha X(antigen CD11C (p150), alpha polypeptide) 5.92 NM_003494 DYSF dysferlin,limb girdle muscular dystrophy 2B (autosomal recessive) 5.85 AI860212PAG1 phosphoprotein associated with glycosphingolipid microdomains 15.75 NM_013447 EMR2 egf-like module containing, mucin-like, hormonereceptor-like 2 5.62 NM_017806 LIME1 Lck interacting transmembraneadaptor 1 5.62 AK092824 AMN Amnionless homolog (mouse) 5.59 AF345567GPR174 G protein-coupled receptor 174 5.26 L03419 FCGR1A; Fc fragment ofIgG, high affinity Ia, receptor LOC440607 (CD64); Fc-gamma receptor I B25.24 BG230586 SLC7A6 solute carrier family 7 (cationic amino acidtransporter, y+ system), member 6 5.18 AF015524 CCRL2 chemokine (C-Cmotif) receptor-like 2 5.13 AA631143 SLC45A3 solute carrier family 45,member 3 5.10 AJ240085 TRAT1 T cell receptor associated transmembraneadaptor 1 5.05 AW183080 GPR92 G protein-coupled receptor 92 5.03NM_002120 HLA-DOB major histocompatibility complex, class II, DO beta5.03 NM_015364 LY96 lymphocyte antigen 96 4.90 NM_020399 GOPC golgiassociated PDZ and coiled-coil motif containing 4.88 AK026133 SEMA4Bsema domain, immunoglobulin domain (Ig), transmembrane domain (TM) andshort cytoplasmic domain, (semaphorin) 4B 4.88 BC041664 VMD2 vitelliformmacular dystrophy 2 (Best disease, bestrophin) 4.85 NM_152592 C14orf49chromosome 14 open reading frame 49 4.85 AA923524 RASGRP4 RAS guanylreleasing protein 4 4.85 BC008777 ITGAL integrin, alpha L (antigen CD11A(p180) 4.67 AF014403 PPAP2A phosphatidic acid phosphatase type 2A 4.65AK097698 SORCS2 Sortilin-related VPS10 domain containing receptor 2 4.63X14355 FCGR1A Fc fragment of IgG, high affinity Ia, receptor (CD64) 4.55NM_001629 ALOX5AP arachidonate 5-lipoxygenase-activating protein 4.50AU155968 C18orf1 chromosome 18 open reading frame 1 4.44 AK075092HERV-FRD HERV-FRD provirus ancestral Env polyprotein 4.42 NM_020960GPR107 G protein-coupled receptor 107 4.37 BC000039 FAM26B family withsequence similarity 26, member B 4.35 NM_153701 IL12RB1 interleukin 12receptor, beta 1 4.35 AI762344 PTGER1 prostaglandin E receptor 1(subtype EP1), 42 kDa 4.31 NM_006459 SPFH1 SPFH domain family, member 14.27 NM_003126 SPTA1 spectrin, alpha, erythrocytic 1 (elliptocytosis 2)4.22 AL518391 AQP1 aquaporin 1 (channel-forming integral protein, 28kDa) 4.12 AK026188 PCDHGC3 protocadherin gamma subfamily C 4.10 AU146685EDG2 Endothelial differentiation, lysophosphatidic acidG-protein-coupled receptor, 2 4.05 BE673587 SLC14A1 Solute carrierfamily 14 (urea transporter), member 1 (Kidd blood group) 4.02 BF129969TSPAN2 tetraspanin 2 4.00 AW243272 KCNK5 Potassium channel, subfamily K,member 5 3.98 T68858 DHRS3 Dehydrogenase/reductase (SDR family) member 33.94 AI827849 VTI1A Vesicle transport through interaction with t- SNAREshomolog 1A (yeast) 3.86 AL134012 NRXN2 Neurexin 2 3.83 BG230614 CD47CD47 antigen (Rh-related antigen, integrin- associated signaltransducer) 3.80 AI869717 MGC15523 hypothetical protein MGC15523 3.80AI458583 SIMP Source of immunodominant MHC-associated peptides 3.79NM_002183 IL3RA interleukin 3 receptor, alpha (low affinity) 3.79AA608820 NRXN2 neurexin 2 3.73 NM_000206 IL2RG interleukin 2 receptor,gamma (severe combined immunodeficiency) 3.72 BC002737 VAMP2vesicle-associated membrane protein 2 (synaptobrevin 2) 3.72 BC005884BID BH3 interacting domain death agonist; BH3 interacting domain deathagonist 3.68 AI688418 PLXNA2 plexin A2 3.68 BC003105 PTP4A3 proteintyrosine phosphatase type IVA, member 3 3.68 NM_001772 CD33 CD33 antigen(gp67) 3.66 AI955119 VAMP2 vesicle-associated membrane protein 2(synaptobrevin 2) 3.65 BC007524 SPAG9 sperm associated antigen 9 3.64AI344200 SLC25A35 solute carrier family 25, member 35 3.64 BC005253KLHL20 kelch-like 20 (Drosophila) 3.58 BF381837 C20orf52 chromosome 20open reading frame 52 3.51 NM_002886 RAP2A; RAP2A, member of RASoncogene family; RAP2B RAP2B, member of RAS oncogene family 3.50NM_007063 TBC1D8 TBC1 domain family, member 8 (with GRAM domain) 3.45AK027160 BCL2L11 BCL2-like 11 (apoptosis facilitator) 3.44 BF055366 EDG2endothelial differentiation, lysophosphatidic acid G-protein-coupledreceptor, 2 3.42 NM_003608 GPR65 G protein-coupled receptor 65 3.41AI675453 PLXNA3 plexin A3 3.40 AV734194 DPP8 dipeptidylpeptidase 8 3.36BC001956 KIAA1961 KIAA1961 gene 3.34 NM_013332 HIG2 hypoxia-inducibleprotein 2 3.31 BC029450 SLC33A1 Solute carrier family 33 (acetyl-CoAtransporter), member 1 3.28 BF677986 KIAA1961 KIAA1961 gene 3.27AI433691 CACNA2D4 calcium channel, voltage-dependent, alpha 2/deltasubunit 4 3.26 AB014573 NPHP4 nephronophthisis 4 3.25 AL582804 LY9lymphocyte antigen 9 3.25 BG236280 CD86 CD86 antigen (CD28 antigenligand 2, B7-2 antigen) 3.24 AA639289 SLC26A7 Solute carrier family 26,member 7 3.24 NM_005211 CSF1R colony stimulating factor 1 receptor,formerly McDonough feline sarcoma viral (v-fms) oncogene homolog; colonystimulating factor 1 receptor, formerly McDonough feline sarcoma viral(v-fms) oncogene homolog 3.24 AI051254 TRPM2 transient receptorpotential cation channel, subfamily M, member 2 3.23 AW292816 ABHD2abhydrolase domain containing 2 3.23 BC040275 RASGRF1 Rasprotein-specific guanine nucleotide-releasing factor 1 3.22 NM_021911GABRB2 gamma-aminobutyric acid (GABA) A receptor, beta 2 3.19 AI660619SLC7A6 solute carrier family 7 (cationic amino acid transporter, y+system), member 6 3.19 NM_001860 SLC31A2 solute carrier family 31(copper transporters), member 2 3.18 NM_015680 C2orf24 chromosome 2 openreading frame 24 3.17 AW058600 SLC36A1 solute carrier family 36(proton/amino acid symporter), member 1 3.16 AU145049 HIP1 Huntingtininteracting protein 1 3.15 NM_005770 SERF2 small EDRK-rich factor 2 3.15NM_003566 EEA1 Early endosome antigen 1, 162 kD 3.14 NM_020041 SLC2A9solute carrier family 2 (facilitated glucose transporter), member 9 3.14W90718 SLC24A4 solute carrier family 24 (sodium/potassium/calciumexchanger), member 4 3.13 AI423165 TICAM2 toll-like receptor adaptormolecule 2 3.12 AI674647 SPPL2A signal peptide peptidase-like 2A 3.11NM_004121 GGTLA1 gamma-glutamyltransferase-like activity 1 3.10NM_004546 NDUFB2 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa 3.05 X15786 RET ret proto-oncogene (multiple endocrine neoplasia andmedullary thyroid carcinoma 1, Hirschsprung disease) 3.05 AF181660 MPZL1myelin protein zero-like 1 3.00 AI571996 STAM2 signal transducingadaptor molecule (SH3 domain and ITAM motif) 2 2.99 NM_000201 ICAM1intercellular adhesion molecule 1 (CD54), human rhinovirus receptor 2.93NM_025244 TSGA10 testis specific, 10 2.93 AU147538 PRKCE Protein kinaseC, epsilon 2.92 NM_024576 OGFRL1 opioid growth factor receptor-like 12.91 AI248055 ABCC4 ATP-binding cassette, sub-family C (CFTR/MRP),member 4 2.86 AA503877 CEPT1 Choline/ethanolamine phosphotransferase 12.84 BC030993 FLJ21127 Hypothetical protein FLJ21127 2.82 NM_001859SLC31A1 solute carrier family 31 (copper transporters), member 1 2.81M74721 CD79A CD79A antigen (immunoglobulin-associated alpha) 2.79AI986112 MGAT4B Mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B 2.79 NM_030930 UNC93B1 unc-93homolog B1 (C. elegans); unc-93 homolog B1 (C. elegans) 2.79 X74039PLAUR plasminogen activator, urokinase receptor 2.75 BC005253 KLHL20kelch-like 20 (Drosophila) 2.73 AB036432 AGER advanced glycosylation endproduct-specific receptor 2.71 NM_007245 ATXN2L ataxin 2-like 2.71NM_016072 GOLT1B golgi transport 1 homolog B (S. cerevisiae) 2.71AI453548 ZDHHC8 zinc finger, DHHC-type containing 8 2.70 AI636233 TMEM8transmembrane protein 8 (five membrane- spanning domains) 2.69 BE502509T3JAM TRAF3 interacting protein 3 2.69 AW117765 PEX13 peroxisomebiogenesis factor 13 2.69 AW052216 IL17RB Interleukin 17 receptor B 2.67NM_003853 IL18RAP interleukin 18 receptor accessory protein 2.66NM_002490 NDUFA6 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6,14 kDa 2.65 NM_016639 TNFRSF12A tumor necrosis factor receptorsuperfamily, member 12A 2.65 AI363185 FLJ20255 Hypothetical proteinFLJ20255 2.65 NM_052931 SLAMF6 SLAM family member 6 2.65 AW571669TNFRSF19L tumor necrosis factor receptor superfamily, member 19-like2.64 AA654142 CEECAM1 cerebral endothelial cell adhesion molecule 1 2.62AW510783 TMEM63A transmembrane protein 63A 2.61 W95007 ACSL4 Acyl-CoAsynthetase long-chain family member 4 2.60 S76475 NTRK3 neurotrophictyrosine kinase, receptor, type 3 2.60 AJ130713 SIGLEC7 sialic acidbinding Ig-like lectin 7 2.56 NM_003775 EDG6 endothelialdifferentiation, G-protein-coupled receptor 6 2.55 AI978986 MAMDC4 MAMdomain containing 4 2.54 AF010447 MR1 major histocompatibility complex,class I-related 2.54 NM_006068 TLR6 toll-like receptor 6 2.53 AF041811NTRK3 neurotrophic tyrosine kinase, receptor, type 3 2.53 AW953521SERF2; small EDRK-rich factor 2; Huntingtin interacting HYPK protein K2.51 AW293276 CD53 CD53 antigen 2.49 AK023058 PLXNA2 Plexin A2 2.49AI125204 C6orf128 chromosome 6 open reading frame 128 2.49 NM_000392ABCC2 ATP-binding cassette, sub-family C (CFTR/MRP), member 2 2.46BC032474 TIRAP toll-interleukin 1 receptor (TIR) domain containingadaptor protein 2.44 NM_031211 IMAA; SLC7A5 pseudogene; SLC7A5pseudogene; LOC388221; NPIP-like locus; NPIP-like locus; hypotheticalLOC440345; protein LOC440345; hypothetical protein LOC440354; LOC440345;PI-3-kinase-related kinase SMG-1 LOC595101; pseudogene;PI-3-kinase-related kinase SMG-1 LOC641298 pseudogene;PI-3-kinase-related kinase SMG-1 pseudogene; PI-3-kinase-related kinaseSMG-1 pseudogene; PI-3-kinase-related kinase SMG-1 - like locus;PI-3-kinase-related kinase SMG-1 - like locus 2.44 AI797836 CD5 CD5antigen (p56-62) 2.41 W72082 C1QR1 complement component 1, qsubcomponent, receptor 1; complement component 1, q subcomponent,receptor 1 2.40 AA708616 DPP9 dipeptidylpeptidase 9 2.40 BM987094 DLGAP4discs, large (Drosophila) homolog-associated protein 4 2.40 AL713719LOC283501 ATPase, Class VI, type 11A 2.39 AI628734 PRLR prolactinreceptor 2.39 NM_012110 CHIC2 cysteine-rich hydrophobic domain 2 2.38AK022002 TFR2 transferrin receptor 2 2.37 NM_001555 IGSF1 immunoglobulinsuperfamily, member 1 2.36 AA426091 C19orf15 chromosome 19 open readingframe 15 2.36 BE547542 GOPC golgi associated PDZ and coiled-coil motifcontaining 2.36 NM_004231 ATP6V1F ATPase, H+ transporting, lysosomal 14kDa, V1 subunit F 2.36 AJ130712 SIGLEC7 sialic acid binding Ig-likelectin 7 2.36 NM_017905 TMCO3 transmembrane and coiled-coil domains 32.35 AB054985 CACNB1 calcium channel, voltage-dependent, beta 1 subunit2.35 NM_005003 NDUFAB1 NADH dehydrogenase (ubiquinone) 1, alpha/betasubcomplex, 1, 8 kDa 2.35 NM_001251 CD68 CD68 antigen 2.35 AA700869PSCD2 Pleckstrin homology, Sec7 and coiled-coil domains 2 (cytohesin-2)2.35 U94903 CD44 CD44 antigen (homing function and Indian blood groupsystem) 2.35 NM_003841 TNFRSF10C tumor necrosis factor receptorsuperfamily, member 10c, decoy without an intracellular domain 2.33NM_004541 NDUFA1 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1,7.5 kDa 2.33 BE567130 KLRK1 Killer cell lectin-like receptor subfamilyK, member 1 2.31 NM_017460 CYP3A4 cytochrome P450, family 3, subfamilyA, polypeptide 4 2.31 AI339536 DSC1 Desmocollin 1 2.31 NM_001783 CD79ACD79A antigen (immunoglobulin-associated alpha); CD79A antigen(immunoglobulin- associated alpha) 2.30 AA333161 VTI1A vesicle transportthrough interaction with t- SNAREs homolog 1A (yeast) 2.30 AW134823 CD6CD6 antigen; CD6 antigen 2.30 AL137537 ATP8B2 ATPase, Class I, type 8B,member 2 2.29 AI671983 SLC2A9 solute carrier family 2 (facilitatedglucose transporter), member 9 2.29 AA018187 C22orf3 chromosome 22 openreading frame 3 2.29 AL117415 ADAM33 ADAM metallopeptidase domain 332.29 NM_002588 PCDHGC3; protocadherin gamma subfamily C, 3; PCDHGB4;protocadherin gamma subfamily B, 4; PCDHGA8; protocadherin gammasubfamily A, 8; PCDHGA12; protocadherin gamma subfamily A, 12; PCDHGC5;protocadherin gamma subfamily C, 5; PCDHGC4; protocadherin gammasubfamily C, 4; PCDHGB7; protocadherin gamma subfamily B, 7; PCDHGB6;protocadherin gamma subfamily B, 6; PCDHGB5; protocadherin gammasubfamily B, 5; PCDHGB3; protocadherin gamma subfamily B, 3; PCDHGB2;protocadherin gamma subfamily B, 2; PCDHGB1; protocadherin gammasubfamily B, 1; PCDHGA11; protocadherin gamma subfamily A, 11; PCDHGA10;protocadherin gamma subfamily A, 10; PCDHGA9; protocadherin gammasubfamily A, 9; PCDHGA7; protocadherin gamma subfamily A, 7; PCDHGA6;protocadherin gamma subfamily A, 6; PCDHGA5; protocadherin gammasubfamily A, 5; PCDHGA4; protocadherin gamma subfamily A, 4; PCDHGA3;protocadherin gamma subfamily A, 3; PCDHGA2; protocadherin gammasubfamily A, 2; PCDHGA1 protocadherin gamma subfamily A, 1 2.29NM_020960 GPR107 G protein-coupled receptor 107 2.29 AK074635 GENX-3414Genethonin 1 2.29 BE138575 ITGB5 Integrin, beta 5 2.28 NM_003830 SIGLEC5sialic acid binding Ig-like lectin 5; sialic acid binding Ig-like lectin5 2.28 NM_013319 UBIAD1 UbiA prenyltransferase domain containing 1 2.28M63889 FGFR1 fibroblast growth factor receptor 1 (fms-related tyrosinekinase 2, Pfeiffer syndrome) 2.27 H67156 MSCP Solute carrier family 25,member 37 2.27 BC006215 SMEK2 KIAA1387 protein; KIAA1387 protein 2.27AL109653 SLITRK2 SLIT and NTRK-like family, member 2 2.27 NM_007011ABHD2 abhydrolase domain containing 2 2.26 AI767210 MGC11332Hypothetical protein MGC11332 2.26 BF723605 NRCAM Neuronal cell adhesionmolecule 2.26 R08129 CDA08 T-cell immunomodulatory protein 2.26 AF052059SEL1L sel-1 suppressor of lin-12-like (C. elegans) 2.26 NM_005729 PPIFpeptidylprolyl isomerase F (cyclophilin F) 2.25 BE858032 ARL2L1ADP-ribosylation factor-like 2-like 1 2.25 AI950390 C14orf118 Chromosome14 open reading frame 118 2.24 NM_017767 SLC39A4 solute carrier family39 (zinc transporter), member 4 2.24 AL110273 SPTAN1 Spectrin, alpha,non-erythrocytic 1 (alpha-fodrin) 2.24 AI077660 CDA08 T-cellimmunomodulatory protein 2.23 AA488687 SLC7A11 solute carrier family 7,(cationic amino acid transporter, y+ system) member 11 2.23 NM_000634IL8RA interleukin 8 receptor, alpha 2.22 AL390177 MGC34032 Solutecarrier family 44, member 5 2.21 NM_001531 MR1 major histocompatibilitycomplex, class I-related 2.21 NM_003183 ADAM17 ADAM metallopeptidasedomain 17 (tumor necrosis factor, alpha, converting enzyme) 2.20AC003999 SCAP2 src family associated phosphoprotein 2 2.20 BC014416SLC33A1 solute carrier family 33 (acetyl-CoA transporter), member 1 2.20AF226731 ADORA3 adenosine A3 receptor 2.19 AI608725 ICAM1 intercellularadhesion molecule 1 (CD54), human rhinovirus receptor 2.19 U41163SLC6A8; solute carrier family 6 (neurotransmitter FLJ43855 transporter,creatine), member 8; similar to sodium- and chloride-dependent creatinetransporter 2.19 AU147799 LRRC15 leucine rich repeat containing 15 2.18AW337166 LOC255104 Transmembrane and coiled-coil domains 4 2.18NM_006505 PVR poliovirus receptor 2.18 AI638420 CLIC4 chlorideintracellular channel 4 2.18 AI167482 SCUBE3 Signal peptide, CUB domain,EGF-like 3 2.18 AI739514 HAS3 hyaluronan synthase 3 2.18 NM_005971 FXYD3FXYD domain containing ion transport regulator 3 2.17 AL022398 TRAF3IP3TRAF3 interacting protein 3 2.17 U90940 FCGR2C Fc fragment of IgG, lowaffinity IIc, receptor for (CD32) 2.16 BC023540 SORCS1 Sortilin-relatedVPS10 domain containing receptor 1 2.16 AV713913 OSTM1 osteopetrosisassociated transmembrane protein 1 2.15 NM_024505 NOX5 NADPH oxidase,EF-hand calcium binding domain 5 2.15 BC006178 SEC22L3 SEC22 vesicletrafficking protein-like 3 (S. cerevisiae); SEC22 vesicle traffickingprotein- like 3 (S. cerevisiae) 2.15 BG151527 GRIK5 glutamate receptor,ionotropic, kainate 5 2.14 AW001754 NEGR1 neuronal growth regulator 12.14 NM_013979 BNIP1 BCL2/adenovirus E1B 19 kDa interacting protein 12.14 NM_018643 TREM1 triggering receptor expressed on myeloid cells 12.12 NM_005284 GPR6 G protein-coupled receptor 6 2.11 AA454190 ZDHHC20zinc finger, DHHC-type containing 20 2.11 AB048796 TMPRSS13transmembrane protease, serine 13 2.11 AL044520 NYD-SP21 testesdevelopment-related NYD-SP21 2.11 BE463930 TMAP1 Matrix-remodellingassociated 7 2.10 NM_152264 SLC39A13 solute carrier family 39 (zinctransporter), member 13 2.08 AL530874 EPHB2 EPH receptor B2 2.07NM_018668 VPS33B vacuolar protein sorting 33B (yeast) 2.07 NM_024531GPR172A G protein-coupled receptor 172A 2.07 NM_023038 ADAM19 ADAMmetallopeptidase domain 19 (meltrin beta) 2.07 BC001281 TNFRSF10B tumornecrosis factor receptor superfamily, member 10b 2.07 AF217749 PCDHB9protocadherin beta 9 2.06 AB030077 FGFR2 fibroblast growth factorreceptor 2 (bacteria- expressed kinase, keratinocyte growth factorreceptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffersyndrome, Jackson-Weiss syndrome) 2.06 AL137432 SUSD1 sushi domaincontaining 1 2.05 NM_004518 KCNQ2 potassium voltage-gated channel,KQT-like subfamily, member 2 2.04 AI672363 VPS33B vacuolar proteinsorting 33B (yeast) 2.04 NM_006671 SLC1A7 solute carrier family 1(glutamate transporter), member 7 2.03 AA215519 DLGAP1 Discs, large(Drosophila) homolog-associated protein 1 2.02 NM_004648 PTPNS1 proteintyrosine phosphatase, non-receptor type substrate 1 2.02 NM_002564 P2RY2purinergic receptor P2Y, G-protein coupled, 2 2.01 BF511678 SCUBE3Signal peptide, CUB domain, EGF-like 3 2.01 BC013385 CLEC7A C-typelectin domain family 7, member A

CD47 Facilitates Engraftment, Inhibits Phagocytosis, and is More HighlyExpressed on AML LSC. It has long been recognized that the innate immunesystem, through natural killer (NK) effector cells, functions in theelimination of non-self and aberrant cells. NK cells eliminate targetcells recognized by a variety of NK cell-activating receptors that bindligands present on many normal cells; however, expression of self majorhistocompatibility complex (MHC) class I molecules can protect a cell bybinding to NK inhibitory receptors.

These inhibitory receptors often contain immunoreceptor tyrosine-basedinhibitory (ITIM) motifs that recruit and activate the SHP-1 and SHP-2tyrosine phosphatases, which in turn inhibit signal transduction fromthe activating receptors. Accumulating evidence indicates thatmonocyte-derived effector cells, such as macrophages and dendriticcells, are also involved in the elimination of non-self and aberrantcells, mediated by a number of activating receptors. These effectorcells also express the inhibitory receptor, signal regulatory proteinalpha (SIRPα), which contains an ITIM motif able to recruit and activatethe SHP-1 and SHP-2 phosphatases resulting in inhibition ofphagocytosis. Several studies have identified CD47 as the ligand forSIRPα. CD47 is a widely expressed transmembrane protein, originallyidentified as integrin associated protein (IAP) due to its physicalassociation with several integrins.

CD47 has been implicated in a number of processes including plateletactivation, cell motility and adhesion, and leukocyte adhesion,migration, and phagocytosis. The CD47-SIRPα interaction has beenimplicated in the inhibition of phagocytosis from a number of studies.First, CD47-deficient, but not wild type, mouse red blood cells (RBCs)were rapidly cleared from the bloodstream by splenic macrophages whentransfused into wild type mice, and this effect was dependent on theCD47-SIRPαcinteraction. CD47-deficient, but not wild type, lymphocytesand bone marrow cells were also rapidly cleared upon transplantationinto congenic wild type recipients through macrophage and dendriticcell-mediated phagocytosis. Additional evidence suggested that theCD47-SIRPoc interaction can inhibit phagocytosis stimulated by therecognition of IgG or complement opsonized cells. Thus, CD47 functionsas a critical regulator of macrophage and dendritic cell phagocytosis bybinding to SIRPα and delivering a dominant inhibitory signal.

We determined expression of CD47 on human AML LSC and normal HSC by flowcytometry. HSC (Lin-CD34+CD38-CD90+) from three samples of normal humanmobilized peripheral blood and AML LSC (Lin-CD34+CD38-CD90−) from sevensamples of human AML were analyzed for surface expression of CD47 (FIG.2). CD47 was expressed at low levels on the surface of normal HSC;however, on average, it was approximately 5-fold more highly expressedon AML LSC, as well as bulk leukemic blasts.

Anti-Human CD47 Monoclonal Antibody Stimulates Phagocytosis and InhibitsEngraftment of AML LSC. In order to test the model that CD47overexpression on AML LSC prevents phagocytosis of these cells throughits interaction with SIRPα on effector cells, we have utilized amonoclonal antibody directed against CD47 known to disrupt theCD47-SIRPα interaction. The hybridoma producing a mouse-anti-human CD47monoclonal antibody, termed B6H12, was obtained from ATCC and used toproduce purified antibody. First, we conducted in vitro phagocytosisassays. Primary human AML LSC were purified by FACS from two samples ofhuman AML, and then loaded with the fluorescent dye CFSE. These cellswere incubated with mouse bone marrow-derived macrophages and monitoredusing immunofluorescence microscopy (FIG. 2) and flow cytometry (FIG. 3)to identify phagocytosed cells. In both cases, no phagocytosis wasobserved in the presence of an isotype control antibody; however,significant phagocytosis was detected with the addition of the anti-CD47antibody. Thus, blockage of human CD47 with a monoclonal antibody iscapable of stimulating the phagocytosis of these cells by mousemacrophages.

We next investigated the ability of the anti-CD47 antibody to inhibitAML LSC engraftment in vivo. Two primary human AML samples were eitheruntreated or coated with the anti-CD47 antibody prior to transplantationinto NOG newborn mice. 13 weeks later, the mice were sacrificed andanalyzed for human leukemia bone marrow engraftment by flow cytometry(FIG. 5). The control mice demonstrated leukemic engraftment while micetransplanted with the anti-CD47-coated cells showed little to noengraftment. These data indicate that blockade of human CD47 with amonoclonal antibody is able to inhibit AML LSC engraftment.

CD96 is a Human Acute Myeloid Leukemia Stem Cell-Specific Cell SurfaceMolecule. CD96, originally termed Tactile, was first identified as a Tcell surface molecule that is highly upregulated upon T cell activation.CD96 is expressed at low levels on resting T and NK cells and isstrongly upregulated upon stimulation in both cell types. It is notexpressed on other hematopoietic cells, and examination of itsexpression pattern showed that it is only otherwise present on someintestinal epithelia. The cytoplasmic domain of CD96 contains a putativeITIM motif, but it is not know if this functions in signal transduction.CD96 promotes adhesion of NK cells to target cells expressing CD155,resulting in stimulation of cytotoxicity of activated NK cells.

Preferential Cell Surface Expression of Molecules Identified from GeneExpression Analysis. Beyond CD47 and CD96, several of the moleculeslisted in FIG. 2B are known to be expressed on AML LSC, including:CD123, CD44, and CD33. The remaining molecules have not been previouslyreported or identified as preferentially expressed on human AML LSCcompared to their normal counterparts. We have examined cell surfaceexpression of two of these molecules by flow cytometry to determine ifthere is preferential expression on AML LSC compared to normal HSC.

In order to evaluate the other candidate genes in FIG. 1B, we screenedthis list for those molecules not likely to be expressed on normal HSCbased on raw array expression values. Next, using published reports, weinvestigated the tissue expression pattern of these genes, in order toidentify those with very restricted patterns of expression for whichmonoclonal antibodies would have few targets besides the leukemia cells.Based on these methods, two promising genes were identified: ParathyroidHormone Receptor 2 and Hepatitis A Virus Cellular Receptor 2 (also knownas TIM-3: T cell immunoglobulin mucin 3). Parathyroid Hormone Receptor 2(PTHR2) is normally expressed in the pancreas and in some areas of thecentral nervous system. Its primary ligand is a peptide termedtuberoinfundibular peptide 39 (TIP39). Hepatitis A Virus CellularReceptor 2 (HAVCR2) is normally expressed on a subset of T lymphocytes.Its primary ligand is a molecule named Galectin-9.

Validation of additional sequences utilize specific antibodies andtesting by flow cytometry, with comparison to normal multipotentprogenitor cells.

Example 2

CD99 is a surface glycoprotein with highest expression on T cells whereit may function in cellular adhesion. CD99 expression on HSC(Lin-CD34+CD38-CD90+) from three samples of normal human cord blood andAML LSC (Lin-CD34+CD38-CD90−) from seven samples of human AML wasdetermined by flow cytometry (FIG. 6). CD99 was expressed at low levelson the surface of normal HSC; however, on average, it is approximately5-fold more highly expressed on AML LSC. CD97 is normally expressed onmost mature hematopoietic cells and is upregulated on activatedlymphocytes where it may function in cellular migration and adhesion.Gene expression profiling indicates low to absent expression of CD97 inHSC and MPP, with approximately 10-fold higher expression in AML LSC.CD97 expression on normal cord blood HSC and AML LSC was examined byflow cytometry and found to be absent on HSC and high on 5 out of 7 AMLLSC samples (FIG. 7).

We examined the surface expression of CD97, CD99, CD180, and TIM3(HAVCR2) on several samples of HSC (from both normal bone marrow andcord blood) and multiple samples of de novo human AML, using flowcytometry. We found increased expression of each of these molecules onAML LSC with low to absent expression on HSC (FIGS. 8-10). We alsoinvestigated the expression of PTH2R in bone marrow HSC and AML LSCusing quantitative real-time PCR, as no monoclonal antibody validatedfor flow cytometry is available for this antigen. We found no expressionof PTHR2 in HSC with increased expression in AML LSC.

Example 3 Prospective Separation of Normal and Leukemic Stem Cells Basedon Differential Expression of TIM-3, a Novel Human AML Stem Cell Marker

Hematopoietic tissues in acute myeloid leukemia (AML) patients containboth leukemia stem cells (LSC) and residual normal hematopoietic stemcells (HSC). The ability to prospectively separate residual HSC from LSCfacilitates scientific and clinical investigation, including purging forautologous hematopoietic cell transplants. We report here theidentification of TIM-3 as a novel AML stem cell surface marker that ishighly expressed on multiple specimens of AML LSC, but not on normalbone marrow HSC. TIM-3 expression was detected in all cytogeneticsubgroups of AML, but was significantly higher in AML-associated withcore binding factor translocations or mutations in CEBPA. By assessingengraftment in NOD/SCID/IL2Rγ-null mice, we determined that normal bonemarrow HSC do not express TIM-3, whereas LSC from multiple AML specimensexpress high levels of TIM-3. Finally, TIM-3 expression enabled theprospective separation of HSC from LSC in multiple primary human AMLsamples.

Cell surface proteins preferentially expressed on AML LSC compared tonormal HSC, include CD123, CD44, CLL-1, CD96, and CD47. Such antigenshave important clinical applications including: targeting withtherapeutic monoclonal antibodies, monitoring of minimal residualdisease by flow cytometry, and prospective separation of LSC and HSC.Monoclonal antibodies targeting several of these antigens have shownpromise in pre-clinical models and are in active clinical developmen.Increased expression of CLL-1 within the Lin-CD34+CD38− compartmentpredicted relapse in two AML patients in remission, suggesting a rolefor LSC surface markers in monitoring minimal residual disease. Thusfar, prospective separation of LSC from HSC has only been reported for asingle patient on the basis of differential expression of CD47.

Here we report the identification of a novel AML stem cell surfacemarker, T-cell immunoglobulin mucin-3 (TIM-3). TIM-3 is normallyexpressed on Th1-T cells, dendritic cells, and monocytes. We found thatTIM-3 is highly expressed on multiple specimens of AML LSC but not onnormal bone marrow HSC. Significantly, differential expression of TIM-3enabled the prospective separation of LSC from HSC in multiple primaryhuman AML samples.

Results

TIM-3 Is More Highly Expressed on AML LSC Than on Normal Bone MarrowHSC. We identified increased expression of TIM-3 in primary human AMLLSC compared to normal bone marrow HSC. On this basis, we investigatedcell surface expression of TIM-3 protein in AML by flow cytometry. TIM-3was more highly expressed on multiple specimens of Lin-CD34+CD38− AMLLSC compared to normal bone marrow HSC; however, TIM-3 expression wasnot significantly different between bulk AML cells and the LSC-enrichedfraction (FIG. 11A, B). Moreover, a greater percentage of Lin-CD34+CD38−cells expressed TIM-3 in multiple specimens of AML than in normal bonemarrow (FIG. 11C). TIM-3 was expressed on 18 out of 20 patient specimensexamined, which consisted of diverse clinical and molecular subtypes.

Because TIM-3 expression was similar on bulk AML cells and theLSC-enriched fraction, we used bulk AML gene expression data from apreviously described cohort of 526 adult AML patients to examine TIM-3expression across cytogenetic and molecularly-defined subgroups of AML.Across cytogenetic subgroups, TIM-3 was more highly expressed in AMLassociated with core binding factor translocations, t(8;21)(q22;q22) andidt(16), but was still detected in samples from other subtypes. InNKAML, no significant associations were identified between TIM-3expression and either FLT3-ITD or NPM1c mutations; however, higher TIM-3expression was detected in the presence of mutations in one or bothcopies of CEBPA.

TIM-3 Is Not Expressed On Functional Normal Bone Marrow HSC. TIM-3expression was detected on a minority of cells within the Lin-CD34+CD38−comparment of normal bone marrow by flow cytometry. To investigate thefunction of TIM-3 expressing cells in this HSC-enriched fraction, weused fluorescence-activated cell sorting (FACS) to purifyLin-CD34+CD38-TIM-3+ and Lin-CD34+CD38-TIM-3− subpopulations of normalbone marrow (FIG. 11D) and assessed each subpopulation bytransplantation into NOD/SCID/IL2Rγ^(null) (NSG) mice. Consistent withHSC function, Lin-CD34+CD38-TIM-3− normal bone marrow cells engraftedlong-term lympho-myeloid hematopoiesis, as indicated by the presence ofhuman CD45+CD19+ lymphoid cells and human CD45+CD33+ myeloid cells inthe bone marrow 12 weeks post-transplant (FIG. 11E). However, at anequal cell dose, Lin-CD34+CD38-TIM-3+ normal bone marrow cells did notengraft lympho-myeloid hematopoiesis, but did engraft one mouse withlymphoid-restricted human CD45+CD19+ cells (FIG. 11E), suggesting thatthis population may contain a downstream multipotent orlymphoid-restricted progenitor. Similar results were obtained with asecond normal bone marrow specimen. In total, 5 out of 7 micetransplanted with Lin-CD34+CD38-TIM3− cells exhibited HSC functioncompared to 0 out of 6 mice transplanted with Lin-CD34+CD38-TIM3+ cells(Table 4A). These results indicate that TIM-3 is not expressed onfunctional normal bone marrow HSC.

TABLE 4 Summary of in vivo engraftment in NSG mice from (A) normal humanbone marrow and (B) primary human AML samples. Lin-CD34+CD38−TIM-3−cells were not detected in AML samples denoted with an (*). (C) Successof prospective isolation of TIM-3− normal HSC from 6 AML samples withresidual normal hematopoietic engraftment detected in NSG mice and 1 AMLsample with residual normal hematopoietic methylcellulose colonyformation activity (^(Y)). A. Lympho- Lymphoid- Cell Myeloid HSCrestricted NBM Sample Cell Population Dose Engraftment Engraftment NBM05Lin-CD34+CD38−TIM-3+ 600 0/3 1/3 Lin-CD34+CD38−TIM-3− 600 2/3 1/3 NBM06Lin-CD34+CD38−TIM-3+ 1230 0/3 0/3 Lin-CD34+CD38−TIM-3− 5500 2/2 0/2 12301/2 1/2 Summary Lin-CD34+CD38−TIM-3+ 0/6 1/6 Lin-CD34+CD38−TIM-3− 5/72/7 B. Cell Leukemic Secondary AML Sample Cell Population DoseEngraftment Engraftment SU001* Lin-CD34+CD38−TIM-3+ 344,000 3/3 SU004*Lin-CD34+CD38−TIM-3+ 240,000 3/3 SU018 Lin-CD34+TIM-3+ 350,000 2/212,000 2/2 2/2 Lin-CD34+TIM-3− 12,000 0/2 SU028* Lin-CD34+CD38−TIM-3+350,000 2/2 22,000 4/4 4/4 SU030 Lin-CD34+CD38−TIM-3+ 200,000 2/2 20,0002/2 Lin-CD34+CD38−TIM-3− 400 0/4 Summary Lin-CD34+(CD38−)TIM-3+ 20/206/6 Lin-CD34+(CD38−)TIM-3− 0/6 C. Prospective Separation of AML SampleResidual Normal HSC TIM-3− HSC SU008 Yes No SU014 Yes No SU030 Yes YesSU031 Yes Yes SU035 Yes No SU036 Yes No SU043  Yes^(Y) Yes

TIM-3 Is Highly Expressed On Functional AML Stem Cells. We nextinvestigated whether TIM-3 was expressed on functional AML stem cellsfrom five patient samples, as defined by the capacity to transplantlong-term leukemic engraftment in NSG mice. In three of these fivecases, all Lin-CD34+CD38− cells were TIM-3+, and eachLin-CD34+CD34-TIM-3+ cell population engrafted NSG mice with leukemia(Table 4B). In one AML sample with heterogeneous TIM-3 expression,FACS-purified Lin-CD34+TIM-3+ cells were able to transplant the diseaseinto primary and secondary NSG recipients, whereas an equal dose ofLin-CD34+TIM-3− cells failed to transplant the disease (FIG. 11F,G).Similarly, functional LSC were contained within the Lin-CD34+CD38-TIM-3+fraction but absent from the the Lin-CD34+CD38-TIM-3− fraction of asecond sample (FIG. 13). In summary, LSC were restricted to the TIM-3+fraction of the Lin-CD34+ or Lin-CD34+CD38− compartment in all fiveengrafting AML samples tested (Table 4B). These results indicate thatTIM-3 is highly expressed on functional AML LSC from multiple patients.

Prospective Separation of Normal HSC From LSC in a Series of AMLPatients. We identified seven primary AML specimens with a highpercentage of leukemia cells (mean and median blast counts of 80% and86% respectively) which exhibited evidence of residual normalhematopoietic stem/progenitor function, as assessed by engraftment oflympho-myeloid hematopoiesis in NSG mice and/or normal erythro-myeloidcolony-forming activity in complete methylcellulose (Table 4C). Becausewe detected TIM-3 expression on functional AML LSC, but not normal bonemarrow HSC, we investigated the ability of differential TIM-3 expressionto discriminate residual normal HSC from LSC in the same patient sample,and permit the prospective separation of these critical stem cellpopulations.

Three of these seven samples had rare TIM-3− populations whichconstituted between 0.04% and 3.7% of the Lin-CD34+CD38− compartment(FIGS. 12A,D and 13A). In each case, Lin-CD34+CD38-TIM3− andLin-CD34+CD38-TIM3+ cells were isolated by FACS and functionally assayedby transplantation in NSG mice and/or colony formation in completemethylcellulose. Each rare TIM3-population exhibited normal HSC functionwith long-term lympho-myeloid engraftment in vivo (FIGS. 12B and 13C)and/or normal methylcellulose colony formation in vitro (FIGS. 12E and13B). To further investigate the relationship between these residualfunctionally normal HSC and the leukemic clone, Lin-CD34+CD38-TIM3−FACS-purified cells, methylcellulose colonies derived from thispopulation, and bone marrow cells from NSG mice engrafted with thispopulation were assessed for the presence of known molecular mutationspresent in the leukemia (FLT3-ITD or inv(16)). In each case, themolecular mutation was detected in the TIM3+ cells but not in the rareTIM-3− cells (FIGS. 12C,F and 13D).

In vivo leukemic engraftment was not observed with two of these samples(SU031 and SU043) despite transplantation of greater than 10⁵ cells inNSG mice (Table 4B), consistent with the previously reported inabilityof some primary human AML specimens to engraft in immunodeficient mice.In contrast, the third sample (SU030) exhibited both normalhematopoietic and leukemic engraftment in NSG mice in vivo. In thiscase, Lin-CD34+CD38-TIM3− cells engrafted FLT3-ITD-negative long-termlympho-myeloid hematopoiesis, whereas Lin-CD34+CD38-TIM3+ cellsengrafted FLT3-ITD-positive long-term myeloid-restricted leukemicengraftment (FIG. 13C,D). Thus, differential TIM-3 expressiondiscriminates residual normal HSC from LSC in these three AML patientsamples (Table 4C), permitting the prospective separation of thesecritical stem cell populations.

We report here the identification of TIM-3 as a novel AML stem cellsurface marker that is highly expressed on multiple specimens of AMLLSC, but not on normal bone marrow HSC. TIM-3 expression was detected inall cytogenetic subgroups of AML, but was significantly higher inAML-associated with core binding factor translocations or mutations inCEBPA. By assessing engraftment in NSG mice, we determined that normalbone marrow HSC do not express TIM-3, whereas LSC from multiple AMLspecimens express high levels of TIM-3. Finally, TIM-3 expressionenabled the prospective separation of HSC from LSC in three out of sevenAML samples with residual normal HSC function.

TIM-3 is normally expressed on Th1-T cells, dendritic cells, andmonocytes, where downstream signal transduction is induced bycross-linking with its ligand Galectin-9 (GAL-9). The GAL-9/TIM-3 axisis a potent regulator of adaptive and innate immune responses. TIM-3 isexpressed at low levels on naive T cells, but is increased upon T cellactivation and differentiation into Th1 cells. GAL-9 binding to TIM-3 onTh1 cells results in activation of NFkB and eventually apoptotic celldeath, and in this way TIM-3 serves to dampen Th1 immune responses. Indendritic cells, TIM-3 signal transduction also stimulates NFkBactivity, which leads to dendritic cell activation rather thanapoptosis. Currently, the signal transduction pathways downstream ofTIM-3 are unknown, but GAL-9 binding to TIM-3 can result in tyrosinephosphorylation of TIM-3.

Elevated TIM-3 expression may directly contribute to AML pathogenesisthrough either a cell-intrinsic mechanism or by disrupting anti-AMLleukocyte activity. One potential cell-intrinsic mechanism involvesstimulation of NFkB activity downstream of TIM-3 signal transduction inLSC. NFkB is active in AML LSC, and several pharmacologic inhibitorshave been shown to have efficacy against primary LSC. Alternatively,TIM-3 may contribute to leukemogenesis by decreasing the concentrationof unbound GAL-9 in the leukemic microenvironment. AttenuatingGAL-9/TIM-3 signaling in infiltrating immune cells may result indecreased macrophage and dendritic cell pro-inflammatory signaling andactivation. We recently demonstrated that phagocytic cells of the innateimmune system, including macrophages and dendritic cells, play a keyrole in leukemic pathogenesis, and that most AML LSC have increasedexpression of CD47 to avoid phagocytosis. Thus, attenuation ofGAL-9/TIM-3 signaling may be an additional mechanism to inhibit theinnate immune response to AML.

In addition to a potential role in leukemic pathogenesis, TIM-3 is anexcellent candidate for AML LSC-targeted therapeutic monoclonalantibodies. The absence of TIM-3 expression on functional normal bonemarrow HSC and residual HSC in AML samples, in contrast to highexpression on multiple samples of AML LSC, provides the rationale fordeveloping such antibodies. Recently, we demonstrated that a blockingmonoclonal antibody directed against CD47, a protein overexpressed onLSC, eliminated AML LSC by stimulating phagocytosis through Fcreceptor-independent mechanisms. In this context, anti-TIM-3 antibodiesable to bind and activate Fc receptors synergize with anti-CD47antibodies to induce more effective phagocytic elimination of AML LSC.

A major result from the current study is the prospective separation ofresidual HSC from AML LSC based on differential expression of TIM-3.Such prospective separation has several clinical applications.Autologous hematopoietic cell transplantation (AHCT) has been utilizedin the treatment of AML, including investigation of protocols employingex vivo chemotherapy to eradicate residual leukemic cells in theautograft. AHCT has fallen out of mainstream clinical practice due toequivalence to conventional chemotherapy. However, purification ofLSC-depleted functionally normal HSC may improve AHCT outcomes andbroaden the use of AHCT to patients who do not achieve completeremission. Second, the ability to differentiate HSC and LSC by flowcytometry enables evaluation of LSC-targeted therapeutics and predictionof relapse based upon minimal residual disease monitoring at the levelof the LSC. This possibility is supported by the demonstration thatincreased expression of the LSC marker CLL-1 in the CD34+CD38− bonemarrow fraction from two AML patients in remission correlated withrelapse.

Lastly, prospective separation of residual functionally normal HSC fromLSC based on TIM-3 expression further provides an opportunity to map theaccumulation of mutations leading to AML. Because leukemogenesisinvolves the multistep accumulation of rare mutations, pre-leukemicmutations likely accumulate in self-renewing HSC. Ultimately, the novelability to prospectively isolate functionally normal HSC from AMLpatients could enable the direct identification of pre-leukemicmutations and may serve as an entry point into observing theaccumulation of leukemogenic events in pre-leukemic HSC.

Materials and Methods

Human Samples. Normal human bone marrow mononuclear cells were purchasedfrom AllCells Inc. (Emeryville, Calif., USA). Human AML samples wereobtained from patients at the Stanford Medical Center with informedconsent, according to IRB-approved protocols (Stanford IRB# 76935 and6453).

Animal Care. All mouse experiments were conducted according to anIACUC-approved protocol and in adherence to the NIH Guide for the Careand Use of Laboratory Animals.

Flow Cytometry Analysis and Cell Sorting. A panel of antibodies was usedfor analysis and sorting of AML LSC (Lin-CD34+CD38−) and HSC(Lin-CD34+CD38-CD90+) as previously described. For AML samples, thelineage consisted of CD3, CD19, and CD20. TIM-3 antibody clone 344823(R&D Systems, Minneapolis, Minn., USA) was used. Human CD34-positivecells were enriched from normal bone marrow by magnetic selection(StemCell Technologies, Vancouver, BC, Canada).

Methylcellulose Colony Assay. Erythro-myeloid colony formation wasassayed by culturing hematopoietic cells in complete methylcellulose(Methocult GF+H4435, Stem Cell Technologies). Colony formation wasassayed after 14 days in culture by microscopy. Colony types scoredwere: CFU-GEMM, colony forming unit—granulocyte, erythrocyte, monocyte,megakaryocyte, BFU-E, blast forming unit—erythrocyte, CFU-E, colonyforming unit—erythrocyte, and CFU-GM—colony forming unit—granulocyte,monocyte.

NSG Xenotransplantation Assay. FACS-purified cell populations weretransplanted into newborn NOD/SCID/IL2Rγ-null (NSG) mice conditionedwith 100 rads of irradiation. After twelve weeks, mice were sacrificedand peripheral blood and bone marrow were analyzed for human myeloidengraftment (hCD45+CD33+) and human lymphoid engraftment (hCD45+CD19+).For secondary transplantation, whole mouse bone marrow cells fromprimary mice containing 10,000 human leukemic cells were transplantedinto irradiated newborn NSG mice and analyzed for engraftment 12 weekslater by flow cytometry.

Microarray Analysis of TIM-3 Expression. Raw Affymetrix CEL files(n=526) were downloaded from NCBI GEO (GSE14468) and normalized usingMAS5 in Bioconductor. Arrays were scaled to median intensity of 500 andtransformed to log2 values. We used a custom CDF (Chip Definition File)to map array 22-mers to Refseq mRNA accessions (44). TIM3/HAVCR2 wasrepresented by the probe summarization corresponding to Refseq accessionNM_032782. NKAML samples (n=219) were identified as having “Normal”karyotype and non-M3 (acute promyelocytic leukemia) FAB subtype.Boxplots of TIM3 expression were generated in R across all karyotypes(n=526), and across FLT3-ITD, NPM1, and CEBPA mutation groups for NKAML(n=219). Association of TIM3 to karyotypic groups and mutational statuswas evaluated by ANOVA.

PCR analysis for inv(16) and FLT3-ITD. Total RNA was isolated by RneasyMicro Kit (Qiagen). cDNA was reverse transcribed with SuperScript IIIFirst-Strand Synthesis Kit (Invitrogen). Inv(16) was detected by PCRwith the following primers: CBFB-C (F) SEQ ID NO:15′-GGGCTGTCTGGAGTTTGATG-3′ and MYH11-B2 (R) SEQ ID NO:25′-TCCTCTTCTCCTCATTCTGCTC-3′. Genomic DNA was isolated by GentraPuregene Cell Kit (Qiagen). FLT3-ITD was detected by PCR with thefollowing primers: FLT3 11F (F) SEQ ID NO:35′-GCAATTTAGGTATGAAAGCCAGC-3′ and FLT3 12R (R) SEQ ID NO:45′-CTTTCAGCATTTTGACGGCAACC-3′.

What is claimed is:
 1. A method for characterizing an acute myeloidleukemia from a patient, the method comprising: contacting a patientsample with reagents specific for a differentially expressed marker orcombination of markers set forth in Table 1; quantitating the number ofmarker expressing cancer cells, wherein the presence of markerexpressing cancer cells is indicative of the presence of AML stem cells(AMLSC).
 2. The method of claim 1, wherein the quantitating is performedby flow cytometry.
 3. The method of claim 1, wherein the quantitating isperformed by immunohistochemistry.
 4. The method of claim 1, wherein thesample is a blood sample.
 5. The method of claim 1, wherein the patienthas been diagnosed as having AML.
 6. The method of claim 5, wherein thepatient is undergoing treatment for AML.
 7. The method according toclaim 1, wherein said patient is a human.
 8. The method of claim 1,wherein the marker is selected from CD97, CD99, CD180 and TIM3.
 9. A kitfor use in the method of claim
 1. 10. A method of screening a candidatechemotherapeutic agent for effectiveness against an AMLSC, the methodcomprising: contacting an AMLSC expressing a polypeptide set forth inTable 1 with a candidate agent, and determining the effectiveness ofsaid agent against said AMLSC.
 11. A method of targeting or depletingAML cancer stem cells, the method comprising contacting reagent bloodcells with an agent that specifically binds a marker or combination ofmarkers set forth in Table 1 in order to target or deplete AMLSC. 12.The method of claim 11, wherein the agent is an antibody.
 13. The methodof claim 11, wherein the the marker is selected from CD97, CD99, CD180and TIM3.
 14. The method of claim 12, wherein the agent is a bispecificantibody that binds two markers set forth in Table
 1. 15. A therapeuticformulation for use in the method of claim
 11. 16. A method for thediagnosis or staging of AML, the method comprising: determining theupregulation of expression of a genetic sequence selected from thoselisted in Table
 1. 17. The method according to claim 16 wherein saiddetermining comprises detecting increased or decreased amounts of mRNAor polypeptide in a sample of cancer cells.
 18. The method according toclaim 16, wherein expression is determined by hybridization to an array.19. The method according to claim 18, wherein said array comprises twoor more sequences set forth in Table 1.